Re: [votca] Relative entropy error in votca

[Christoph Junghans]

On Tue, Apr 23, 2024 at 3:22 PM SAYAN DUTTA  wrote:
>
> Here with I am attaching inverse.log and settings.xml file.
Thanks, I understand the error, but it seems nobody has ever done
relative entropy with pressure correction, hence it is not
implemented.
I think the way you could make that work is to do one iteration
without pressure correction and then change the settings file and add
it back.
Use at your own risk!

Christoph
>
> On Tue, Apr 23, 2024 at 11:55 PM Christoph Junghans  
> wrote:
>>
>> On Tue, Apr 23, 2024 at 2:52 PM SAYAN DUTTA  wrote:
>> >
>> > Here is the part of inverse.log which is throwing the error:
>> Send the full file, I want to look at the output to run_gromacs.sh as
>> well above the error as well.
>>
>> Christoph
>>
>> > For all non-bonded
>> > for_all: run 'do_external post_update_single re' for interaction named 
>> > 'CG-CG'
>> > Running subscript 'post_update_re_single.sh' (from tags post_update_single 
>> > re) dir /home/sdutta/Softwares/votca-2024/share/votca/scripts/inverse
>> > csg_get_property: No value for 'cg.inverse.restart_file' found in 
>> > /home/sdutta/Project/CG-simulation-with-REM/settings.xml, trying 
>> > /home/sdutta/Softwares/votca-2024/share/votca/xml/csg_defaults.xml
>> > csg_get_property: value for 'cg.inverse.restart_file' from 
>> > /home/sdutta/Softwares/votca-2024/share/votca/xml/csg_defaults.xml: 
>> > restart_points.log
>> > Postupd tasks for CG-CG: scale pressure smooth
>> > Doing postupd task 'scale' for 'CG-CG'
>> > Running critical command 'mv CG-CG.pot.new CG-CG.pot.1'
>> > Running subscript 'postupd_scale.sh CG-CG.pot.1 CG-CG.pot.new' (from tags 
>> > postupd scale) dir 
>> > /home/sdutta/Softwares/votca-2024/share/votca/scripts/inverse
>> > scaling potential for CG-CG update by factor 0.5
>> > Running subscript 'table_linearop.pl CG-CG.pot.1 CG-CG.pot.new 0.5 0' 
>> > (from tags table linearop) dir 
>> > /home/sdutta/Softwares/votca-2024/share/votca/scripts/inverse
>> > table_linearop.pl: CG-CG.pot.1 to CG-CG.pot.new with y' = 0.5*y + 0
>> > Doing postupd task 'pressure' for 'CG-CG'
>> > Running critical command 'mv CG-CG.pot.new CG-CG.pot.2'
>> > Running subscript 'postupd_pressure.sh CG-CG.pot.2 CG-CG.pot.new' (from 
>> > tags postupd pressure) dir 
>> > /home/sdutta/Softwares/votca-2024/share/votca/scripts/inverse
>> > csg_get_property: No value for 'cg.inverse.gromacs.g_energy.topol' found 
>> > in /home/sdutta/Project/CG-simulation-with-REM/settings.xml, trying 
>> > /home/sdutta/Softwares/votca-2024/share/votca/xml/csg_defaults.xml
>> > csg_get_property: returning emtpy value for 
>> > 'cg.inverse.gromacs.g_energy.topol'
>> > csg_get_property: No value for 'cg.inverse.gromacs.topol' found in 
>> > /home/sdutta/CG-simulation-with-REM/settings.xml, trying 
>> > /home/sdutta/Softwares/votca-2024/share/votca/xml/csg_defaults.xml
>> > csg_get_property: value for 'cg.inverse.gromacs.topol' from 
>> > /home/sdutta/Softwares/votca-2024/share/votca/xml/csg_defaults.xml: 
>> > topol.tpr
>> >
>> > Callstack:
>> > /home/sdutta/Softwares/votca-2024/share/votca/scripts/inverse/inverse.sh - 
>> > linenumber 161
>> > do_external - linenumber 182 in 
>> > /home/sdutta/Softwares/votca-2024/share/votca/scripts/inverse/functions_common.sh
>> > 
>> > /home/sdutta/Softwares/votca-2024/share/votca/scripts/inverse/prepare_re.sh
>> >  - linenumber 40
>> > critical - linenumber 4 (see 'csg_call --cat function 
>> > critical')
>> > do_external - linenumber 19 (see 'csg_call --cat function 
>> > do_external')
>> > 
>> > /home/sdutta/Softwares/votca-2024/share/votca/scripts/inverse/post_update_generic.sh
>> >  - linenumber 31
>> > for_all - linenumber 22 (see 'csg_call --cat 
>> > function for_all')
>> > do_external - linenumber 19 (see 'csg_call 
>> > --cat function do_external')
>> > 
>> > /home/sdutta/Softwares/votca-2024/share/votca/scripts/inverse/post_update_re_single.sh
>> >  - linenumber 44
>> > do_external - linenumber 1

Re: [votca] Relative entropy error in votca

[Christoph Junghans]

  
>  #
> ####
> die: (called from 3578195)  CSG_MASTER_PID is 3576660
> die: pids to kill: 3576660 3577748 3577924 3578030 3578044 3578133 3578195
>
> On Tuesday, April 23, 2024 at 10:53:16 PM UTC+2 Christoph Junghans wrote:
>>
>> On Tue, Apr 23, 2024 at 11:58 AM SAYAN DUTTA  wrote:
>> >
>> > Thank you Christoph, this seems to be working, but I am trying to apply 
>> > pressure correction with the potentials obtained from relative entropy. I 
>> > assume since works same like ibi, I added the pressure correction with 
>> > settings.xml file as follows :
>> > 
>> > 
>> > CG-CG.dist.tgt
>> > 
>> > 1.0
>> > 
>> > 0 1 0
>> > 
>> > scale pressure smooth
>> > 
>> > 0.5
>> > 
>> > simple
>> > 1 0 1
>> > 
>> > 0.001
>> > 
>> > 
>> > 
>> > 5
>> > 
>> > 
>> >
>> > with this I am encountering a error like this : calc_pressure_gromacs.sh: 
>> > Gromacs tpr file 'topol.tpr' not found
>> > can you please help me with the possible modifications based on this error
>> Not a 100% sure, can you post your inverse.log?
>>
>> Christoph
>> >
>> >
>> >
>> > On Mon, Apr 22, 2024 at 10:59 PM Christoph Junghans  
>> > wrote:
>> >>
>> >> On Mon, Apr 22, 2024 at 11:41 AM SAYAN DUTTA  wrote:
>> >> >
>> >> > Hi Cristoph, I want to ask you this second question once again, because 
>> >> > based on the implementation of relative entropy it seems quite 
>> >> > important to start with initial_guess properly
>> >> > I did this part as following way:
>> >> > settings.xml file
>> >> >
>> >> > 
>> >> >
>> >> > 
>> >> > CG-CG
>> >> > CG
>> >> > CG
>> >> > 0
>> >> > 1.5
>> >> > 0.01
>> >> > true
>> >> > 
>> >> >
>> >> > 
>> >> > So this is giving me the potential of mean force- CG-CG.force.new by 
>> >> > csg_stat (PMF)
>> >> > Then I am using CSG_resample as follows:
>> >> > csg_resample --in CG-CG.force.new --out CG-CG.param.init --grid 
>> >> > 0:0.02:1.5
>> >> > But I am very much doubtful in this way of doing it, because apparently 
>> >> > csg_resample can do the linear extrapolation in non-sampled region, but 
>> >> > non-bonded interactions entry can be extrapolated asymptotically with 
>> >> > some other functions if I am thinking correctly. This will be very much 
>> >> > helpful to me if you mark some hints in my way of estimating the 
>> >> > initial guess because with this obtained intitial guess I am 
>> >> > encountering the problem like negative Hessian matrix, which is failing 
>> >> > with further iterations
>> >> For preparation of the potential see: 
>> >> https://www.votca.org/csg/preparing.html
>> >> Just to clarify the param.init files contain the spline parameters or
>> >> parameter of the , just for cbspl it is similar to the
>> >> forces.
>> >>
>> >> Christoph
>> >>
>> >> > On Sunday, April 21, 2024 at 2:21:34 AM UTC+2 Christoph Junghans wrote:
>> >> >>
>> >> >> On Sat, Apr 20, 2024 at 6:10 PM SAYAN DUTTA  
>> >> >> wrote:
>> >> >> >
>> >> >> > Hi Christoph, Thank you so much for your reply, I tried to figure it 
>> >> >> > out by couple of possible ways, but failing for unknown reasons. 
>> >> >> > Just trying to understand a couple of viewpoints in terms of working 
>> >> >> > with the relative entropy based framework with votca--
>> >> >> > 1. In the tutorial of spce/re with gromacs I found table.xvg which I 
>> >> >> > need to copy at every folder though for running simulation I only 
>> >> >> > need table_CG_CG.xvg(obtained from RE iterations), then what is the 
>> >> >> > exact role of the extra table?
>> >> >> Older versions of Gromacs needed that table for all intera

Re: [votca] Relative entropy error in votca

[Christoph Junghans]

On Tue, Apr 23, 2024 at 11:58 AM SAYAN DUTTA  wrote:
>
> Thank you Christoph, this seems to be working, but I am trying to apply 
> pressure correction with the potentials obtained from relative entropy. I 
> assume since works same like ibi, I added the pressure correction with 
> settings.xml file as follows :
> 
>   
>   CG-CG.dist.tgt
>   
>1.0
>
>0 1 0
>
>scale pressure smooth
>
>  0.5
>  
>simple
>1 0 1
>
>  0.001
>
>  
>   
>  5
>  
>
>
> with this I am encountering a error like this : calc_pressure_gromacs.sh: 
> Gromacs tpr file 'topol.tpr' not found
> can you please help me with the possible modifications based on this error
Not a 100% sure, can you post your inverse.log?

Christoph
>
>
>
> On Mon, Apr 22, 2024 at 10:59 PM Christoph Junghans  
> wrote:
>>
>> On Mon, Apr 22, 2024 at 11:41 AM SAYAN DUTTA  wrote:
>> >
>> > Hi Cristoph, I want to ask you this second question once again, because 
>> > based on the implementation of relative entropy it seems quite important 
>> > to start with initial_guess properly
>> > I did this part as following way:
>> > settings.xml file
>> >
>> > 
>> >
>> >   
>> > CG-CG
>> > CG
>> > CG
>> > 0
>> > 1.5
>> > 0.01
>> > true
>> >   
>> >
>> > 
>> > So this is giving me the potential of mean force- CG-CG.force.new by 
>> > csg_stat (PMF)
>> > Then I am using CSG_resample as follows:
>> > csg_resample --in CG-CG.force.new --out CG-CG.param.init --grid 0:0.02:1.5
>> > But I am very much doubtful in this way of doing it, because apparently 
>> > csg_resample can do the linear extrapolation in non-sampled region, but 
>> > non-bonded interactions entry can be extrapolated asymptotically with some 
>> > other functions if I am thinking correctly. This will be very much helpful 
>> > to me if you mark some hints in my way of estimating the initial guess 
>> > because with this obtained intitial guess I am encountering the problem 
>> > like negative Hessian matrix, which is failing with further iterations
>> For preparation of the potential see: 
>> https://www.votca.org/csg/preparing.html
>> Just to clarify the param.init files contain the spline parameters or
>> parameter of the , just for cbspl it is similar to the
>> forces.
>>
>> Christoph
>>
>> > On Sunday, April 21, 2024 at 2:21:34 AM UTC+2 Christoph Junghans wrote:
>> >>
>> >> On Sat, Apr 20, 2024 at 6:10 PM SAYAN DUTTA  wrote:
>> >> >
>> >> > Hi Christoph, Thank you so much for your reply, I tried to figure it 
>> >> > out by couple of possible ways, but failing for unknown reasons. Just 
>> >> > trying to understand a couple of viewpoints in terms of working with 
>> >> > the relative entropy based framework with votca--
>> >> > 1. In the tutorial of spce/re with gromacs I found table.xvg which I 
>> >> > need to copy at every folder though for running simulation I only need 
>> >> > table_CG_CG.xvg(obtained from RE iterations), then what is the exact 
>> >> > role of the extra table?
>> >> Older versions of Gromacs needed that table for all interactions that
>> >> weren't covered by the energy group pairs listed in the mdp, even if
>> >> the rest group was empty. I believe gromacs 2019 can do without it.
>> >>
>> >> > 2. Do I need to take any special care for setting my Intial guess, I 
>> >> > was apperntly extrapolating the pair potential to get CG-CG.param.init, 
>> >> > Do I need to follow any specific way to get the initial guess parameters
>> >> Yes, these are just the parameter from a fit of the PMF to the tabulated 
>> >> form.
>> >>
>> >> > 3. Based on the current implementaion of re in votca, can I employ this 
>> >> > for more than one non-bonded interactions?
>> >> Yes, see the methanol-water/X_* examples.
>> >>
>> >> Christoph
>> >>
>> >> > Please help me with this details
>> >> >
>> >> > On Friday, April 19, 2024 at 2:30:46 AM UTC+2 Christoph Junghans wrote:
>> >> >>
>> >> >> On Thu, Apr 18, 2024 at 6:

Re: [votca] Relative entropy error in votca

[Christoph Junghans]

On Mon, Apr 22, 2024 at 11:41 AM SAYAN DUTTA  wrote:
>
> Hi Cristoph, I want to ask you this second question once again, because based 
> on the implementation of relative entropy it seems quite important to start 
> with initial_guess properly
> I did this part as following way:
> settings.xml file
>
> 
>
>   
> CG-CG
> CG
> CG
> 0
> 1.5
> 0.01
> true
>   
>
> 
> So this is giving me the potential of mean force- CG-CG.force.new by csg_stat 
> (PMF)
> Then I am using CSG_resample as follows:
> csg_resample --in CG-CG.force.new --out CG-CG.param.init --grid 0:0.02:1.5
> But I am very much doubtful in this way of doing it, because apparently 
> csg_resample can do the linear extrapolation in non-sampled region, but 
> non-bonded interactions entry can be extrapolated asymptotically with some 
> other functions if I am thinking correctly. This will be very much helpful to 
> me if you mark some hints in my way of estimating the initial guess because 
> with this obtained intitial guess I am encountering the problem like negative 
> Hessian matrix, which is failing with further iterations
For preparation of the potential see: https://www.votca.org/csg/preparing.html
Just to clarify the param.init files contain the spline parameters or
parameter of the , just for cbspl it is similar to the
forces.

Christoph

> On Sunday, April 21, 2024 at 2:21:34 AM UTC+2 Christoph Junghans wrote:
>>
>> On Sat, Apr 20, 2024 at 6:10 PM SAYAN DUTTA  wrote:
>> >
>> > Hi Christoph, Thank you so much for your reply, I tried to figure it out 
>> > by couple of possible ways, but failing for unknown reasons. Just trying 
>> > to understand a couple of viewpoints in terms of working with the relative 
>> > entropy based framework with votca--
>> > 1. In the tutorial of spce/re with gromacs I found table.xvg which I need 
>> > to copy at every folder though for running simulation I only need 
>> > table_CG_CG.xvg(obtained from RE iterations), then what is the exact role 
>> > of the extra table?
>> Older versions of Gromacs needed that table for all interactions that
>> weren't covered by the energy group pairs listed in the mdp, even if
>> the rest group was empty. I believe gromacs 2019 can do without it.
>>
>> > 2. Do I need to take any special care for setting my Intial guess, I was 
>> > apperntly extrapolating the pair potential to get CG-CG.param.init, Do I 
>> > need to follow any specific way to get the initial guess parameters
>> Yes, these are just the parameter from a fit of the PMF to the tabulated 
>> form.
>>
>> > 3. Based on the current implementaion of re in votca, can I employ this 
>> > for more than one non-bonded interactions?
>> Yes, see the methanol-water/X_* examples.
>>
>> Christoph
>>
>> > Please help me with this details
>> >
>> > On Friday, April 19, 2024 at 2:30:46 AM UTC+2 Christoph Junghans wrote:
>> >>
>> >> On Thu, Apr 18, 2024 at 6:05 PM SAYAN DUTTA  wrote:
>> >> >
>> >> > Hi, I am facing a trouble for running re, I am trying to use relative 
>> >> > entropy framework for liquid methanol (single site coarse grained 
>> >> > model), I am getting this error after 2nd iteration
>> >> > table_average.sh: averaging with awk failed
>> >> > CG-simulation-with-REM/step_001/A-A.param.cur.9Dv5'
>> >> > x-value mismatch 0.03125 vs. 0.03 in line 2
>> >> > Based on this error can you please suggest me any possible mistakes>
>> >> > I tried with the tutorial of spce, it worked fine. But this error I am 
>> >> > getting for other systems like methanol.
>> >> > Please let me know possible solutions of this problem
>> >> A mismatch in x value usually hints at a problem in your settings.xml
>> >> file, or one of the input files is at a different spacing.
>> >> Hard to say, I would try to delete step_000 and step_001 and start over.
>> >>
>> >> Christoph
>> >> >
>> >> > --
>> >> > Join us on Slack: https://join.slack.com/t/votca/signup
>> >> > ---
>> >> > You received this message because you are subscribed to the Google 
>> >> > Groups "votca" group.
>> >> > To unsubscribe from this group and stop receiving emails from it, send 
>> >> > an email to votca+un...@googlegroups.com.
>> >> > To view this discussion on the web visit 
>> >> > https://groups.google.com/d

Re: [votca] Relative entropy error in votca

[Christoph Junghans]

On Sat, Apr 20, 2024 at 6:10 PM SAYAN DUTTA  wrote:
>
> Hi Christoph, Thank you so much for your reply, I tried to figure it out by 
> couple of possible ways, but failing for unknown reasons. Just trying to 
> understand a couple of viewpoints in terms of working with the relative 
> entropy based framework with votca--
> 1. In the tutorial of spce/re with gromacs I found table.xvg which I need to 
> copy at every folder though for running simulation I only need 
> table_CG_CG.xvg(obtained from RE iterations), then what is the exact role of 
> the extra table?
Older versions of Gromacs needed that table for all interactions that
weren't covered by the energy group pairs listed in the mdp, even if
the rest group was empty. I believe gromacs 2019 can do without it.

> 2. Do I need to take any special care for setting my Intial guess, I was 
> apperntly extrapolating the pair potential to get CG-CG.param.init, Do I need 
> to follow any specific way to get the initial guess parameters
Yes, these are just the parameter from a fit of the PMF to the tabulated form.

> 3. Based on the current implementaion of re in votca, can I employ this for 
> more than one non-bonded interactions?
Yes, see the methanol-water/X_* examples.

Christoph

> Please help me with this details
>
> On Friday, April 19, 2024 at 2:30:46 AM UTC+2 Christoph Junghans wrote:
>>
>> On Thu, Apr 18, 2024 at 6:05 PM SAYAN DUTTA  wrote:
>> >
>> > Hi, I am facing a trouble for running re, I am trying to use relative 
>> > entropy framework for liquid methanol (single site coarse grained model), 
>> > I am getting this error after 2nd iteration
>> > table_average.sh: averaging with awk failed
>> > CG-simulation-with-REM/step_001/A-A.param.cur.9Dv5'
>> > x-value mismatch 0.03125 vs. 0.03 in line 2
>> > Based on this error can you please suggest me any possible mistakes>
>> > I tried with the tutorial of spce, it worked fine. But this error I am 
>> > getting for other systems like methanol.
>> > Please let me know possible solutions of this problem
>> A mismatch in x value usually hints at a problem in your settings.xml
>> file, or one of the input files is at a different spacing.
>> Hard to say, I would try to delete step_000 and step_001 and start over.
>>
>> Christoph
>> >
>> > --
>> > Join us on Slack: https://join.slack.com/t/votca/signup
>> > ---
>> > You received this message because you are subscribed to the Google Groups 
>> > "votca" group.
>> > To unsubscribe from this group and stop receiving emails from it, send an 
>> > email to votca+un...@googlegroups.com.
>> > To view this discussion on the web visit 
>> > https://groups.google.com/d/msgid/votca/b1bc18b7-8382-4c41-a65e-fc79e212b1cen%40googlegroups.com.
>>
>>
>>
>> --
>> Christoph Junghans
>> Web: http://www.compphys.de
>
> --
> Join us on Slack: https://join.slack.com/t/votca/signup
> ---
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> To unsubscribe from this group and stop receiving emails from it, send an 
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-- 
Christoph Junghans
Web: http://www.compphys.de

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Re: [votca] Relative entropy error in votca

[Christoph Junghans]

On Thu, Apr 18, 2024 at 6:05 PM SAYAN DUTTA  wrote:
>
> Hi, I am facing a trouble for running re, I am trying to use relative entropy 
> framework for liquid methanol (single site coarse grained model), I am 
> getting this error after 2nd iteration
> table_average.sh: averaging with awk failed
> CG-simulation-with-REM/step_001/A-A.param.cur.9Dv5'
> x-value mismatch 0.03125 vs.  0.03  in line 2
> Based on this error can you please suggest me any possible mistakes>
> I tried with the tutorial of spce, it worked fine. But this error I am 
> getting for other systems like methanol.
> Please let me know possible solutions of this problem
A mismatch in x value usually hints at a problem in your settings.xml
file, or one of the input files is at a different spacing.
Hard to say, I would try to delete step_000 and step_001 and start over.

Christoph
>
> --
> Join us on Slack: https://join.slack.com/t/votca/signup
> ---
> You received this message because you are subscribed to the Google Groups 
> "votca" group.
> To unsubscribe from this group and stop receiving emails from it, send an 
> email to votca+unsubscr...@googlegroups.com.
> To view this discussion on the web visit 
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-- 
Christoph Junghans
Web: http://www.compphys.de

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Re: [votca] Using LAMMPS with VOTCA

[Christoph Junghans]

On Wed, Apr 3, 2024 at 5:28 PM 'JIANXIN HE' via votca
 wrote:
>
> Dear Christoph,
>
> Thank you for your clear explanation!!! I have successfully utilized VOTCA 
> for mapping LAMMPS (all atom) following your guidance, specifically using the 
> command:
> csg_map --top topol.xml --trj lammps.data --cg mapping.xml --out lmp_cg.dump
> I have a small question regarding the output from --out lmp_cg.dump. Is it 
> possible to export this data back into a LAMMPS data file format? If so, how 
> can I specify the styles for the data file? I did not find detailed 
> instructions in the manual.
No, that is not implemented.

> While using csg_dump --top lammps.data > log, I noticed a kind warning 
> indicating that the VOTCA LAMMPS data reader supports certain styles (angle, 
> atom, bond, full, molecule).
> Or it only --out the dump file? Thank you for your assistance.
That is correct, the lammps reader can only digest certain styles in
the input file.

For both issues, patches are welcome, after all VOTCA is open-source.

Christoph

>
> Best,
> J.
> On Monday, February 21, 2022 at 4:50:12 PM UTC-6 Christoph Junghans wrote:
>>
>> On Mon, Feb 21, 2022 at 3:08 PM Satyen Dhamankar  wrote:
>> >
>> > Furthermore, where is the resname DUM coming from?
>> It is the residue name and as data file have no residue name, VOTCA
>> sets it to DUM for dummy.
>>
>> >
>> > On Monday, February 21, 2022 at 4:54:43 PM UTC-5 Satyen Dhamankar wrote:
>> >>
>> >> Oh sorry for the misunderstanding. I have already run a SPCE simulation 
>> >> in LAMMPS. I wanted to get the coarse-grained initial config using 
>> >> csg_map, however, i am not sure how to go about making the mapping.xml 
>> >> file using the current directions that you have.
>> >>
>> >> This is what I see when I run csg_dump --top sys.data, this is what I see:
>> >> ```
>> >> WARNING: The votca lammps data reader is only able to read lammps files 
>> >> formatted in the following styles:
>> >> angle
>> >> atom
>> >> bond
>> >> full
>> >> molecule
>> >>
>> >> These styles use the following formats in the atom block:
>> >> atom-ID molecule-ID atom-type charge x y z
>> >> atom-ID molecule-ID atom-type charge x y z nx ny nz
>> >> atom-ID molecule-ID atom-type x y z
>> >> atom-ID molecule-ID atom-type x y z nx ny nz
>> >> atom-ID atom-type x y z
>> >> atom-ID atom-type x y z nx ny nz
>> >>
>> >> I have 2187 beads in 729 molecules
>> >> Boundary Condition: orthorhombic
>> >> Box matix: 2.8 0 0
>> >> 0 2.8 0
>> >> 0 0 2.8
>> >>
>> >> List of residues:
>> >> 0 name: DUM id: 0
>> >> 1 name: DUM id: 1
>> >> 2 name: DUM id: 2
>> >> 3 name: DUM id: 3
>> >> 4 name: DUM id: 4
>> >> 5 name: DUM id: 5
>> >> 6 name: DUM id: 6
>> >> 7 name: DUM id: 7
>> >> 8 name: DUM id: 8
>> >> 9 name: DUM id: 9
>> >> ...
>> >> List of molecules:
>> >> molecule: 1 H2O1 beads: 3
>> >> 0 Name O1 Type O1 Mass 15.9994 Resnr 0 Resname DUM Charge -0.82
>> >> 1 Name H2 Type H2 Mass 1.008 Resnr 0 Resname DUM Charge 0.41
>> >> 2 Name H2 Type H2 Mass 1.008 Resnr 0 Resname DUM Charge 0.41
>> >> molecule: 2 H2O1 beads: 3
>> >> 3 Name O1 Type O1 Mass 15.9994 Resnr 1 Resname DUM Charge -0.82
>> >> 4 Name H2 Type H2 Mass 1.008 Resnr 1 Resname DUM Charge 0.41
>> >> 5 Name H2 Type H2 Mass 1.008 Resnr 1 Resname DUM Charge 0.41
>> >> molecule: 3 H2O1 beads: 3
>> >> ...
>> >> ```
>> >> Reading the above, molecule name is H2O1. What I dont get, is that the H2 
>> >> molecules are exactly the same, except for the sr no. If i have a larger 
>> >> molecule without symmetric hydrogens, I imagine the program will not be 
>> >> able to distinguish. How should I go about making the xml file?
>> I think for more complicated molecule, you will need to create xml
>> topology file.
>> See towards the end of
>> https://www.votca.org/csg/input_files.html#advanced-topology-handling.
>>
>> You can basically do something like:
>> $ cat topol.xml
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> then you can use H20:O1 etc in the mapping file. (Check with csg_dump
>> --top topol.xml first.)
>>
>> inferring all topology in

Re: [votca] segmentation error in csg_stat

[Christoph Junghans]

I don't think the min and max matter much at this stage, you will just
get a lot of zeros in the histogram. Once you start IBI you will have
to set them more carefully.

Christoph

On Sun, Mar 31, 2024 at 5:07 AM Pratyasha Bhardwaj
 wrote:
>
> Dear Christoph,
>
> Thank you for pointing that out. What about setting the minimum and maximum 
> distance. Do we set the maximum in the settings file for rdf calculation 
> according to the force cutoff we used in the all-atomistic simulation?
>
> Sincerely,
> Pratyasha
>
> On Sat, Mar 30, 2024 at 7:32 PM Christoph Junghans  wrote:
>>
>> On Wed, Mar 27, 2024 at 5:29 AM Pratyasha Bhardwaj
>>  wrote:
>> >
>> > Dear Users,
>> >
>> > I have been trying to obtain the rdfs for my system. however, I get 
>> > segmentation fault:
>> > begin to calculate distribution functions
>> > # of bonded interactions: 0
>> > # of non-bonded interactions: 10
>> > Segmentation fault
>> >
>> > 1. I have a doubt about the minimum and maximum values to be entered in 
>> > the settings file. How do I decide on that?
>> > 2. My system has 2 different molecules and 4 different atom types. My 
>> > mapping scheme is almost 1 Kuhn segment representing 1 CG bead. Thus, for 
>> > a polyethylene molecule, 1 CG bead will represent about 5 ethylene 
>> > monomers. Is it incorrect to  use such high level coarse graining if I 
>> > want to use IBI
>> > 3. I was able to obtain the bond and angle potentials using csg_boltzmann. 
>> > However, the error comes when I use csg_stat. Where am i going wrong? What 
>> > does this error mean?
>> In your settings file you are reusing the name "POL-POL" 6x, but
>> interaction names need to be unique. That might cause the segfault.
>>
>> Christoph
>> >
>> > I am attaching my files here. The trajectory,gro file and tpr file can be 
>> > found using this link: 
>> > https://drive.google.com/drive/u/0/folders/10MOUsNZqZctHYm8ithO7wndp1rzaQiAe
>> > Any help will be really appreciated.
>> >
>> > Thank you
>> > Sincerely,
>> > Pratyasha
>> >
>> > --
>> > Join us on Slack: https://join.slack.com/t/votca/signup
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>> > To unsubscribe from this group and stop receiving emails from it, send an 
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>> > https://groups.google.com/d/msgid/votca/c85d77b1-3d00-498c-9794-d864fd50d146n%40googlegroups.com.
>>
>>
>>
>> --
>> Christoph Junghans
>> Web: http://www.compphys.de
>>
>> --
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>
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Re: [votca] segmentation error in csg_stat

[Christoph Junghans]

On Wed, Mar 27, 2024 at 5:29 AM Pratyasha Bhardwaj
 wrote:
>
> Dear Users,
>
> I have been trying to obtain the rdfs for my system. however, I get 
> segmentation fault:
> begin to calculate distribution functions
> # of bonded interactions: 0
> # of non-bonded interactions: 10
> Segmentation fault
>
> 1. I have a doubt about the minimum and maximum values to be entered in the 
> settings file. How do I decide on that?
> 2. My system has 2 different molecules and 4 different atom types. My mapping 
> scheme is almost 1 Kuhn segment representing 1 CG bead. Thus, for a 
> polyethylene molecule, 1 CG bead will represent about 5 ethylene monomers. Is 
> it incorrect to  use such high level coarse graining if I want to use IBI
> 3. I was able to obtain the bond and angle potentials using csg_boltzmann. 
> However, the error comes when I use csg_stat. Where am i going wrong? What 
> does this error mean?
In your settings file you are reusing the name "POL-POL" 6x, but
interaction names need to be unique. That might cause the segfault.

Christoph
>
> I am attaching my files here. The trajectory,gro file and tpr file can be 
> found using this link: 
> https://drive.google.com/drive/u/0/folders/10MOUsNZqZctHYm8ithO7wndp1rzaQiAe
> Any help will be really appreciated.
>
> Thank you
> Sincerely,
> Pratyasha
>
> --
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Re: [votca] Mapping Block-copolymer

[Christoph Junghans]

On Wed, Mar 13, 2024 at 6:17 AM Pratyasha Bhardwaj
 wrote:
>
> Dear Christopher,
>
> Other_chain_A is actually the name of the all-atom topology file(It has the 
> .itp extension). It is not a molecule, it is the name of the file that 
> contains all information regarding the PEX,PEY,PEZ,PEW and PEG molecules.
> When I do csg_dump --top new.tpr, I have the following output(a portion of 
> that):
> molecule: 255 Other_chain_B beads: 123
Looks like the molecule is named "Other_chain_B".

> 31242 Name 1:PEX:CA Type CT3 Mass 12.011 Resnr 0 Resname PEX Charge -0.27
> 31243 Name 1:PEX:HA1 Type HA3 Mass 1.008 Resnr 0 Resname PEX Charge 0.09
> 31244 Name 1:PEX:HA2 Type HA3 Mass 1.008 Resnr 0 Resname PEX Charge 0.09
> 31245 Name 1:PEX:HA3 Type HA3 Mass 1.008 Resnr 0 Resname PEX Charge 0.09
> 31246 Name 1:PEX:CB Type CT2 Mass 12.011 Resnr 0 Resname PEX Charge -0.18
> 31247 Name 1:PEX:HB1 Type HA2 Mass 1.008 Resnr 0 Resname PEX Charge 0.09
> 31248 Name 1:PEX:HB2 Type HA2 Mass 1.008 Resnr 0 Resname PEX Charge 0.09
> 31249 Name 1:PEX:CC Type CT2 Mass 12.011 Resnr 0 Resname PEX Charge -0.18
> 31250 Name 1:PEX:HC1 Type HA2 Mass 1.008 Resnr 0 Resname PEX Charge 0.09
> 31251 Name 1:PEX:HC2 Type HA2 Mass 1.008 Resnr 0 Resname PEX Charge 0.09
> 31252 Name 1:PEX:CD Type CT2 Mass 12.011 Resnr 0 Resname PEX Charge -0.18
> 31253 Name 1:PEX:HD1 Type HA2 Mass 1.008 Resnr 0 Resname PEX Charge 0.09
> 31254 Name 1:PEX:HD2 Type HA2 Mass 1.008 Resnr 0 Resname PEX Charge 0.09
> 31255 Name 1:PEX:CE Type CT2 Mass 12.011 Resnr 0 Resname PEX Charge -0.18
> 31256 Name 1:PEX:HE1 Type HA2 Mass 1.008 Resnr 0 Resname PEX Charge 0.09
> 31257 Name 1:PEX:HE2 Type HA2 Mass 1.008 Resnr 0 Resname PEX Charge 0.09
> 31258 Name 1:PEX:CF Type CT2 Mass 12.011 Resnr 0 Resname PEX Charge -0.18
> 31259 Name 1:PEX:HF1 Type HA2 Mass 1.008 Resnr 0 Resname PEX Charge 0.09
> 31260 Name 1:PEX:HF2 Type HA2 Mass 1.008 Resnr 0 Resname PEX Charge 0.09
> 31261 Name 1:PEX:CG Type CT2 Mass 12.011 Resnr 0 Resname PEX Charge -0.18
> And hence in the end, I obtain a msg  'I have 0 beads in 0 molecules for the 
> coarsegraining'
> How do I fix this? Should I use the 2 .itp files I have in place of the .tpr 
> file I have been using?
VOTCA can only read tpr files, another option is to write your own
topology.xml file.

Christoph
>
> Thank You
> Sincerely,
> Pratyasha
>
> On Tue, Mar 12, 2024 at 5:53 PM Christoph Junghans  wrote:
>>
>> On Tue, Mar 12, 2024 at 12:03 AM Pratyasha Bhardwaj
>>  wrote:
>> >
>> > Dear Christopher,
>> >
>> > I have made all the mapping files. I have a total of 5 different 
>> > molecules, namely: PEW,PEX,PEY,PEZ(all polyethylene molecules) and PEG. I 
>> > haven't defined the bonds in coarse-grained topology yet as you mentioned 
>> > above.
>> > However, when I try to use the csg_map function -> csg_map --top new.tpr 
>> > --trj changedALL.gro --cg "PEG.xml;PEX.xml;PEY.xml;PEZ.xml;PEW.xml" --out 
>> > conf_cg.gro, I get this error: WARNING: unknown molecule "Other_chain_A" 
>> > with id 2817 in topology
>> > molecule will not be mapped to CG representation
>> > Check weather a mapping file for all molecule exists, was specified in 
>> > --cg separated by ; and the ident tag in xml-file matches the molecule name
>> It is a warning about an unmapped molecule just ignore it, if you
>> don't want "Other_chain_A" be mapped otherwise you will have to create
>> one more xml file.
>>
>> Chirstoph
>> >
>> > During creation of topology, I had created 2 itp files that contains the 
>> > topology information. I am attaching those itp files as well as all other 
>> > files used in the command. Can you point out where I might be making a 
>> > mistake as I have defined all the molecules.
>> > Since the gro file is exceeding the upload limit. I am attaching a link 
>> > for the gro file and tpr file 
>> > :https://drive.google.com/drive/u/0/folders/10MOUsNZqZctHYm8ithO7wndp1rzaQiAe
>> >
>> > Sincerely,
>> > Pratyasha
>> >
>> > On Sunday, February 4, 2024 at 11:36:53 PM UTC+5:30 Christoph Junghans 
>> > wrote:
>> >>
>> >> On Sun, Feb 4, 2024 at 9:47 AM Pratyasha Bhardwaj
>> >>  wrote:
>> >> >
>> >> > Dear Christoph,
>> >> >
>> >> > Thank you for the quick reply. What I meant is I have a gro file where 
>> >> > the PE molecules are named as PEX , PEY and so on, each having 
>> >> > different length and then I have PEG molecule. I have bonds between the 
>> >> > different PE a

Re: [votca] Re: averaging from awk failed

[Christoph Junghans]

On Tue, Mar 12, 2024 at 8:00 AM dd ding  wrote:

> hi Christoph
>
> I had the same issue, can you tell me how you fixed it at the time?
>
> [image: bug.png]
>
> This issue was from 2013 and has been fixed a long time ago, I need a bit
more context to help here.

Christoph


> yours
> ddd
> 在2013年10月1日星期二 UTC+8 04:21:36 写道：
>
>> Hi Sikandar,
>>
>> I found it, there was a typo in awk script, so the error message got
>> lost, but the error was valid.
>> The x values of the two param files mismatch and hence
>> table_average.sh, gives an error.
>>
>> Cheers,
>>
>> Christoph
>>
>> 2013/9/30 Sikandar Mashayak :
>> > Hi Christoph
>> >
>> > Please find attached the step_001/CG-CG.param.cur and
>> > step_002/CG-CG.param.cur.
>> >
>> > Thanks
>> > Sikandar
>> >
>> >
>> > On Mon, Sep 30, 2013 at 10:42 AM, Sikandar Mashayak 
>>
>> > wrote:
>> >>
>> >> Hi
>> >>
>> >> I am trying to make sure SPC/E water relative entropy tutorial works
>> well
>> >> after I made few modifications to csg code.
>> >>
>> >> However, I am getting the table averaging error:
>> >>
>> >> table_average.sh: averaging with awk failed
>> >>
>> >> The log file is attached.
>> >>
>> >> Not sure why this error occurring in step_002 while averaging seems to
>> >> have worked well for step_001.
>> >>
>> >> I guess, once this is issue is resolved, it should be ok to merge
>> >> 'sikandar' branch to 'default'.
>> >>
>> >> Thanks
>> >> Sikandar
>> >
>> >
>> > --
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>> > "votca" group.
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>> > email to votca+un...@googlegroups.com.
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>> > For more options, visit https://groups.google.com/groups/opt_out.
>>
>>
>>
>> --
>> Christoph Junghans
>> Web: http://www.compphys.de
>>
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Re: [votca] Mapping Block-copolymer

[Christoph Junghans]

On Tue, Mar 12, 2024 at 12:03 AM Pratyasha Bhardwaj
 wrote:
>
> Dear Christopher,
>
> I have made all the mapping files. I have a total of 5 different molecules, 
> namely: PEW,PEX,PEY,PEZ(all polyethylene molecules) and PEG. I haven't 
> defined the bonds in coarse-grained topology yet as you mentioned above.
> However, when I try to use the csg_map function -> csg_map --top new.tpr 
> --trj changedALL.gro --cg "PEG.xml;PEX.xml;PEY.xml;PEZ.xml;PEW.xml" --out 
> conf_cg.gro, I get this error: WARNING: unknown molecule "Other_chain_A" with 
> id 2817 in topology
> molecule will not be mapped to CG representation
> Check weather a mapping file for all molecule exists, was specified in --cg 
> separated by ; and the ident tag in xml-file matches the molecule name
It is a warning about an unmapped molecule just ignore it, if you
don't want "Other_chain_A" be mapped otherwise you will have to create
one more xml file.

Chirstoph
>
> During creation of topology, I had created 2 itp files that contains the 
> topology information. I am attaching those itp files as well as all other 
> files used in the command. Can you point out where I might be making a 
> mistake as I have defined all the molecules.
> Since the gro file is exceeding the upload limit. I am attaching a link for 
> the gro file and tpr file 
> :https://drive.google.com/drive/u/0/folders/10MOUsNZqZctHYm8ithO7wndp1rzaQiAe
>
> Sincerely,
> Pratyasha
>
> On Sunday, February 4, 2024 at 11:36:53 PM UTC+5:30 Christoph Junghans wrote:
>>
>> On Sun, Feb 4, 2024 at 9:47 AM Pratyasha Bhardwaj
>>  wrote:
>> >
>> > Dear Christoph,
>> >
>> > Thank you for the quick reply. What I meant is I have a gro file where the 
>> > PE molecules are named as PEX , PEY and so on, each having different 
>> > length and then I have PEG molecule. I have bonds between the different PE 
>> > and PEG chains forming a large copolymer chain. If I define one mapping 
>> > file per molecule, how will I account for the bonds between these 
>> > different molecules.
>>
>> Votca doesn't support bonds between different molecules, but you can
>> also map the PE* parts separately and then reintroduce the bonds in
>> the coarse-grained topology by hand.
>>
>> Christoph
>>
>> >
>> > Thank you
>> > Pratyasha
>> >
>> >
>> > On Sunday, February 4, 2024 at 9:07:35 PM UTC+5:30 Christoph Junghans 
>> > wrote:
>> >>
>> >> On Sun, Feb 4, 2024 at 8:16 AM Pratyasha Bhardwaj
>> >>  wrote:
>> >> >
>> >> > Dear Users,
>> >> >
>> >> > How do I map a block copolymer in votca? My all-atom system has PE- PEG 
>> >> > copolymer chains and water. Since PE and PEG are bonded to each other , 
>> >> > how do I define the mapping file?
>> >> See here: https://www.votca.org/csg/input_files.html#mapping-files
>> >>
>> >> > What do I put in the 'ident' tag in the xml file.
>> >> It is the name of the molecule from the topology file.
>> >>
>> >> > Could you please help me out?
>> >> You could try to use Stock as well: http://stock.cmm.ki.si/smt/
>> >>
>> >> Christoph
>> >> >
>> >> > Thank You
>> >> > Pratyasha
>> >> >
>> >> > --
>> >> > Join us on Slack: https://join.slack.com/t/votca/signup
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>> >> > an email to votca+un...@googlegroups.com.
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>> >> > https://groups.google.com/d/msgid/votca/1255ccc8-b8fc-4ce9-8287-1a5fb1f498d0n%40googlegroups.com.
>> >>
>> >>
>> >>
>> >> --
>> >> Christoph Junghans
>> >> Web: http://www.compphys.de
>> >
>> > --
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Re: [votca] Distributions with Iterative Boltzmann Inversion and LAMMPS

[Christoph Junghans]

On Fri, Mar 1, 2024 at 09:14 'Joerg-Ruediger Hill' via votca <
votca@googlegroups.com> wrote:

> Dear Christoph,
> thanks again for your answer. The problem was in the LAMMPS structure
> file. All beads have to be sorted by molecule for VOTCA to work correctly.
> LAMMPS itself has no problems with other sort orders. Maybe this could be
> added to the VOTCA manual.
>
Ok thanks for the information, could you open an issue on GitHub with a
small example, so we can try to fix that?

Thanks,

Christoph

>
> Best Regards,
> Jörg
>
>
> Christoph Junghans schrieb am Freitag, 1. März 2024 um 02:01:43 UTC+1:
>
>> On Thu, Feb 29, 2024 at 07:36 'Joerg-Ruediger Hill' via votca <
>> vo...@googlegroups.com> wrote:
>>
>>> Dear Christoph,
>>> thanks for the quick answer. As I understood there should be bonds and
>>> angles defined in the topology file, which was indeed not the case.
>>> However, adding them (as in the file attached) makes no difference in
>>> the outcome. If I compare the target distribution and the distribution
>>> after the first iteration for the B1/B1 nonbond interaction I have peaks
>>> for the bonds only in the distribution from the first iteration (see
>>> figure).
>>> Similiarly, if I do the same for the B1-B2 bond there are no peaks at
>>> around 2.5 Ang in the distribution from the first iteration.
>>> Do I have to add some keywords to make exclusions?
>>>
>> Unfortunately not, you can check the exclusions with csg_dump —excl.
>>
>> You should also restrict the min and max of the interaction.
>>
>> Christoph
>>
>>>
>>> Best Regards,
>>> Jörg
>>> [image: B1_B1.png][image: B1-B2.png]
>>>
>>> Christoph Junghans schrieb am Mittwoch, 28. Februar 2024 um 16:20:58
>>> UTC+1:
>>>
>>>> On Wed, Feb 28, 2024 at 06:36 'Joerg-Ruediger Hill' via votca <
>>>> vo...@googlegroups.com> wrote:
>>>>
>>>>> I have been trying to run Iterative Boltzmann Inversion with LAMMPS on
>>>>> a test hexane system as in the original VOTCA paper. However, the
>>>>> iterations stop in the first cycle since there is an obvious mismatch of
>>>>> the original distributions generated with csg_stat and the distributions
>>>>> generated in the iterations. In particular, the peaks for the B1-B2 bonds
>>>>> (around 2.5 Ang) show up in all distributions for the non-bonded
>>>>> interactions and the distribution for the B1-B2 bond is the one for the
>>>>> B2/B2 non-bonded interaction. Obviously, there is a problem with matching
>>>>> the correct interactions.
>>>>> How does csg_inverse figure out where the bonds should be in the CG
>>>>> simulation? I have attached all my files.
>>>>>
>>>> the bonds are read from the topology file, in case of lammps you will
>>>> need to make a xml topology to define bonds (and exclusions for the
>>>> non-bonded interactions). Without the exclusions you might get artificial
>>>> peaks in the rdfs.
>>>>
>>>> Christoph
>>>>
>>>>>
>>>>> --
>>>>> Join us on Slack: https://join.slack.com/t/votca/signup
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>>>>> an email to votca+un...@googlegroups.com.
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>>>>> .
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Re: [votca] Distributions with Iterative Boltzmann Inversion and LAMMPS

[Christoph Junghans]

On Thu, Feb 29, 2024 at 07:36 'Joerg-Ruediger Hill' via votca <
votca@googlegroups.com> wrote:

> Dear Christoph,
> thanks for the quick answer. As I understood there should be bonds and
> angles defined in the topology file, which was indeed not the case.
> However, adding them (as in the file attached) makes no difference in the
> outcome. If I compare the target distribution and the distribution
> after the first iteration for the B1/B1 nonbond interaction I have peaks
> for the bonds only in the distribution from the first iteration (see
> figure).
> Similiarly, if I do the same for the B1-B2 bond there are no peaks at
> around 2.5 Ang in the distribution from the first iteration.
> Do I have to add some keywords to make exclusions?
>
Unfortunately not, you can check the exclusions with csg_dump —excl.

You should also restrict the min and max of the interaction.

Christoph

>
> Best Regards,
> Jörg
> [image: B1_B1.png][image: B1-B2.png]
>
> Christoph Junghans schrieb am Mittwoch, 28. Februar 2024 um 16:20:58 UTC+1:
>
>> On Wed, Feb 28, 2024 at 06:36 'Joerg-Ruediger Hill' via votca <
>> vo...@googlegroups.com> wrote:
>>
>>> I have been trying to run Iterative Boltzmann Inversion with LAMMPS on a
>>> test hexane system as in the original VOTCA paper. However, the iterations
>>> stop in the first cycle since there is an obvious mismatch of the original
>>> distributions generated with csg_stat and the distributions generated in
>>> the iterations. In particular, the peaks for the B1-B2 bonds (around 2.5
>>> Ang) show up in all distributions for the non-bonded interactions and the
>>> distribution for the B1-B2 bond is the one for the B2/B2 non-bonded
>>> interaction. Obviously, there is a problem with matching the correct
>>> interactions.
>>> How does csg_inverse figure out where the bonds should be in the CG
>>> simulation? I have attached all my files.
>>>
>> the bonds are read from the topology file, in case of lammps you will
>> need to make a xml topology to define bonds (and exclusions for the
>> non-bonded interactions). Without the exclusions you might get artificial
>> peaks in the rdfs.
>>
>> Christoph
>>
>>>
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>>>
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Re: [votca] Distributions with Iterative Boltzmann Inversion and LAMMPS

[Christoph Junghans]

On Wed, Feb 28, 2024 at 06:36 'Joerg-Ruediger Hill' via votca <
votca@googlegroups.com> wrote:

> I have been trying to run Iterative Boltzmann Inversion with LAMMPS on a
> test hexane system as in the original VOTCA paper. However, the iterations
> stop in the first cycle since there is an obvious mismatch of the original
> distributions generated with csg_stat and the distributions generated in
> the iterations. In particular, the peaks for the B1-B2 bonds (around 2.5
> Ang) show up in all distributions for the non-bonded interactions and the
> distribution for the B1-B2 bond is the one for the B2/B2 non-bonded
> interaction. Obviously, there is a problem with matching the correct
> interactions.
> How does csg_inverse figure out where the bonds should be in the CG
> simulation? I have attached all my files.
>
the bonds are read from the topology file, in case of lammps you will need
to make a xml topology to define bonds (and exclusions for the non-bonded
interactions). Without the exclusions you might get artificial peaks in the
rdfs.

Christoph

>
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> 
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Re: [votca] CG mapping of molecule with symmetrical topology

[Christoph Junghans]

On Sun, Feb 25, 2024, 21:14 Roozbeh R  wrote:

> Hi,
> I have also a question regarding order of atoms listing in cg bead
> definition in the mapping file. Is it safe to say that it is NOT a
> mandatory requirement by votca to list the atomistic beads which are mapped
> to a cg bead in the topology section of the mapping file in a
> weight-descending order? obviously it seems votca prefers that to be the
> case based on examples and tutorials & actually i tested it already in
> hexane tutorial , via flipping the order in which a carbon and a hydrogen
> atoms are listed in mapping of one of the beads (naturally did the same to
> the weights) and it seems it is not causing any problems for converting AA
> to CG. Still i would rather reconfirm it here now than notice sth is wrong
> later. and  if my thinking is right, is this descending listing some sort
> of a speed booster for faster mapping of atomistic trajectory into a cg
> one?
>
The order doesn't matter! Also no speed loss.

Christoph

thank you for the clarification.
> roozi
>
> On Wednesday, February 21, 2024 at 5:44:49 PM UTC+3:30 Christoph Junghans
> wrote:
>
>> On Tue, Feb 20, 2024 at 3:49 PM Roozbeh R  wrote:
>> >
>> > Well am not very efficient in coding ,but i think it is worth giving it
>> a shot . so would you please point to where shall i begin for this specific
>> case of resid initiation? i already checked votca source and found :
>> "~\votca\csg\src\tools\csg_map.cc" . Is this the file to be modified? and
>> if so, shall i modify some other CC files/headers/etc. too?
>> I think you have two options: modify the mapper in
>> csg/src/libcsg/map.cc or modify the writer in
>> csg/src/libcsg/modules/io/pdbwriter.cc.
>>
>> Christoph
>>
>> > kindly please advise,
>> >
>> > On Wednesday, February 21, 2024 at 1:28:20 AM UTC+3:30 Christoph
>> Junghans wrote:
>> >>
>> >> On Tue, Feb 20, 2024 at 4:17 PM Roozbeh R  wrote:
>> >> >
>> >> > Hi Christoph,
>> >> > Thank you for the reply. Ok, I see.
>> >> > One more question arises regarding Topology file of atomistic model:
>> my protein pdb file (and hence topology file) starts from resid 392 (as its
>> been extracted from a bigger protein fragment) . when i run csg_map, an
>> error message appear regarding the first atom mapped to the CG bead :
>> molecule 392:GLY:N does not exist . when i check AA topology input of
>> votca, via csg_dump --top topol.tpr, however i can see that the first atom
>> identifier is: 0 Name 1:GLY:N Type NH3 Mass 14.007 Resnr 0 Resname GLY
>> Charge -0.3 , which means votca disregards the resid as listed in the
>> original topology file, in which the first resid is 392, and reset/initiate
>> res ids from 1. this is quite problematic for a case like mine as all
>> topology/coordinate files are automatically generated base on data banks
>> info / XRD files.
>> >> > so i wonder is there a workaround to make votca consider residues
>> resids as written in the topology file and not reset them to start from 1?
>> >> Nope, no workaround, but you should be able to hack VOTCA's source to
>> >> do what you want pretty easily.
>> >>
>> >> Christoph
>> >>
>> >> > kind regards,
>> >> >
>> >> > On Tuesday, February 20, 2024 at 5:54:56 PM UTC+3:30 Christoph
>> Junghans wrote:
>> >> >>
>> >> >> On Sun, Feb 18, 2024 at 11:47 PM Roozbeh R 
>> wrote:
>> >> >> >
>> >> >> > Dear All,
>> >> >> > I intend to prepare a cg topology file for a peptide fragment
>> which is a symmetrical molecule i.e. there is two copies of each residue in
>> the atomistic model of my molecule albeit with different segment id in the
>> pdb file. I wish to map the atomistic model to a cg model in which each of
>> the symmetrical parts is mapped into a separate cg bead. i wonder how can i
>> make votca consider each of these redundant residues as part of a separate
>> CG bead, because in the mapping section of the example topology files of
>> votca tutorials, each atom mapped to the cg bead is designated by a "resid:
>> resname :atomname" combination which in my case would point to 2 different
>> atoms (each with a different segment id in the atomistic model ,e.g. PROA
>> vs PROB) so actually this it is not sufficient to point to the one specific
>> atom, instead it will point to 2 atoms which leaves me wondering how (and
>> if) votca can understand which atom belongs to whic

Re: [votca] CG mapping of molecule with symmetrical topology

[Christoph Junghans]

On Tue, Feb 20, 2024 at 3:49 PM Roozbeh R  wrote:
>
> Well am not very efficient in coding ,but i think it is worth giving it a 
> shot .  so would you please point to where shall i begin for this specific 
> case of resid initiation? i already checked votca source and found : 
> "~\votca\csg\src\tools\csg_map.cc" . Is this the file to be modified? and if 
> so, shall i modify some other CC files/headers/etc. too?
I think you have two options: modify the mapper in
csg/src/libcsg/map.cc or modify the writer in
csg/src/libcsg/modules/io/pdbwriter.cc.

Christoph

>  kindly please advise,
>
> On Wednesday, February 21, 2024 at 1:28:20 AM UTC+3:30 Christoph Junghans 
> wrote:
>>
>> On Tue, Feb 20, 2024 at 4:17 PM Roozbeh R  wrote:
>> >
>> > Hi Christoph,
>> > Thank you for the reply. Ok, I see.
>> > One more question arises regarding Topology file of atomistic model: my 
>> > protein pdb file (and hence topology file) starts from resid 392 (as its 
>> > been extracted from a bigger protein fragment) . when i run csg_map, an 
>> > error message appear regarding the first atom mapped to the CG bead : 
>> > molecule 392:GLY:N does not exist . when i check AA topology input of 
>> > votca, via csg_dump --top topol.tpr, however i can see that the first atom 
>> > identifier is: 0 Name 1:GLY:N Type NH3 Mass 14.007 Resnr 0 Resname GLY 
>> > Charge -0.3 , which means votca disregards the resid as listed in the 
>> > original topology file, in which the first resid is 392, and 
>> > reset/initiate res ids from 1. this is quite problematic for a case like 
>> > mine as all topology/coordinate files are automatically generated base on 
>> > data banks info / XRD files.
>> > so i wonder is there a workaround to make votca consider residues resids 
>> > as written in the topology file and not reset them to start from 1?
>> Nope, no workaround, but you should be able to hack VOTCA's source to
>> do what you want pretty easily.
>>
>> Christoph
>>
>> > kind regards,
>> >
>> > On Tuesday, February 20, 2024 at 5:54:56 PM UTC+3:30 Christoph Junghans 
>> > wrote:
>> >>
>> >> On Sun, Feb 18, 2024 at 11:47 PM Roozbeh R  wrote:
>> >> >
>> >> > Dear All,
>> >> > I intend to prepare a cg topology file for a peptide fragment which is 
>> >> > a symmetrical molecule i.e. there is two copies of each residue in the 
>> >> > atomistic model of my molecule albeit with different segment id in the 
>> >> > pdb file. I wish to map the atomistic model to a cg model in which each 
>> >> > of the symmetrical parts is mapped into a separate cg bead. i wonder 
>> >> > how can i make votca consider each of these redundant residues as part 
>> >> > of a separate CG bead, because in the mapping section of the example 
>> >> > topology files of votca tutorials, each atom mapped to the cg bead is 
>> >> > designated by a "resid: resname :atomname" combination which in my case 
>> >> > would point to 2 different atoms (each with a different segment id in 
>> >> > the atomistic model ,e.g. PROA vs PROB) so actually this it is not 
>> >> > sufficient to point to the one specific atom, instead it will point to 
>> >> > 2 atoms which leaves me wondering how (and if) votca can understand 
>> >> > which atom belongs to which bead in this case? will it choose between 
>> >> > the 2 atoms randomly ? or is there a method to further articulate 
>> >> > atom/cg bead association?
>> >>
>> >> VOTCA (and GROMACS) use some form of "resid:resname:atomname" as an
>> >> identifier, if that is not unique for your case, you will have to
>> >> change your topology, so it can be mapped by csg_map. Or write the
>> >> topology file by hand without mapping.
>> >>
>> >> Christoph
>> >> >
>> >> > thank you for the valuable support,
>> >> > Roozi
>> >> >
>> >> > --
>> >> > Join us on Slack: https://join.slack.com/t/votca/signup
>> >> > ---
>> >> > You received this message because you are subscribed to the Google 
>> >> > Groups "votca" group.
>> >> > To unsubscribe from this group and stop receiving emails from it, send 
>> >> > an email to votca+un...@googlegroups.com.
>> >> > To view this discussion on the web visit 
>> >&

Re: [votca] CG mapping of molecule with symmetrical topology

[Christoph Junghans]

On Tue, Feb 20, 2024 at 4:17 PM Roozbeh R  wrote:
>
> Hi Christoph,
> Thank you for the reply. Ok, I see.
> One more question arises regarding Topology file of atomistic model: my 
> protein pdb file (and hence topology file) starts from resid 392 (as its been 
> extracted from a bigger protein fragment) . when i run  csg_map, an error 
> message appear regarding the first atom mapped to the CG bead :  molecule 
> 392:GLY:N does not exist . when i check AA topology input of votca, via 
> csg_dump --top topol.tpr, however i can see that the first atom identifier 
> is: 0 Name 1:GLY:N Type NH3 Mass 14.007 Resnr 0 Resname GLY Charge -0.3 , 
> which means votca disregards the resid as listed in the original topology 
> file, in which the first resid is 392, and reset/initiate res ids from 1. 
> this is quite problematic for a case like mine as all topology/coordinate 
> files are automatically generated base on data banks info / XRD files.
> so i wonder is there a workaround to make votca consider residues resids as 
> written in the topology file and not reset them to start from 1?
Nope, no workaround, but you should be able to hack VOTCA's source to
do what you want pretty easily.

Christoph

> kind regards,
>
> On Tuesday, February 20, 2024 at 5:54:56 PM UTC+3:30 Christoph Junghans wrote:
>>
>> On Sun, Feb 18, 2024 at 11:47 PM Roozbeh R  wrote:
>> >
>> > Dear All,
>> > I intend to prepare a cg topology file for a peptide fragment which is a 
>> > symmetrical molecule i.e. there is two copies of each residue in the 
>> > atomistic model of my molecule albeit with different segment id in the pdb 
>> > file. I wish to map the atomistic model to a cg model in which each of the 
>> > symmetrical parts is mapped into a separate cg bead. i wonder how can i 
>> > make votca consider each of these redundant residues as part of a separate 
>> > CG bead, because in the mapping section of the example topology files of 
>> > votca tutorials, each atom mapped to the cg bead is designated by a 
>> > "resid: resname :atomname" combination which in my case would point to 2 
>> > different atoms (each with a different segment id in the atomistic model 
>> > ,e.g. PROA vs PROB) so actually this it is not sufficient to point to the 
>> > one specific atom, instead it will point to 2 atoms which leaves me 
>> > wondering how (and if) votca can understand which atom belongs to which 
>> > bead in this case? will it choose between the 2 atoms randomly ? or is 
>> > there a method to further articulate atom/cg bead association?
>>
>> VOTCA (and GROMACS) use some form of "resid:resname:atomname" as an
>> identifier, if that is not unique for your case, you will have to
>> change your topology, so it can be mapped by csg_map. Or write the
>> topology file by hand without mapping.
>>
>> Christoph
>> >
>> > thank you for the valuable support,
>> > Roozi
>> >
>> > --
>> > Join us on Slack: https://join.slack.com/t/votca/signup
>> > ---
>> > You received this message because you are subscribed to the Google Groups 
>> > "votca" group.
>> > To unsubscribe from this group and stop receiving emails from it, send an 
>> > email to votca+un...@googlegroups.com.
>> > To view this discussion on the web visit 
>> > https://groups.google.com/d/msgid/votca/dd98f37a-768f-4d5d-be37-29c42b48120bn%40googlegroups.com.
>>
>>
>>
>> --
>> Christoph Junghans
>> Web: http://www.compphys.de
>
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Re: [votca] CG mapping of molecule with symmetrical topology

[Christoph Junghans]

On Sun, Feb 18, 2024 at 11:47 PM Roozbeh R  wrote:
>
> Dear All,
> I intend to prepare a cg topology file for a peptide fragment which is a 
> symmetrical molecule i.e. there is two copies of each residue in the 
> atomistic model of my molecule albeit with different segment id in the pdb 
> file. I wish to map the atomistic model to a cg model in which each of the 
> symmetrical parts is mapped into a separate cg bead. i wonder how can i  make 
> votca consider each of these redundant residues as part of a separate CG 
> bead, because in the mapping section of the example topology files of votca 
> tutorials, each atom mapped to the cg bead is designated  by  a "resid: 
> resname :atomname" combination which in my case would point to 2 different 
> atoms (each with a different segment id in the atomistic model ,e.g. PROA vs 
> PROB) so  actually this it is not sufficient to point to the one specific 
> atom, instead it will point to 2 atoms which leaves me wondering  how (and 
> if) votca can understand which atom belongs  to which bead in this case? will 
> it choose between the 2 atoms randomly ? or is there a method to further 
> articulate atom/cg bead association?

VOTCA (and GROMACS) use some form of "resid:resname:atomname" as an
identifier, if that is not unique for your case, you will have to
change your topology, so it can be mapped by csg_map. Or write the
topology file by hand without mapping.

Christoph
>
> thank you for the valuable support,
> Roozi
>
> --
> Join us on Slack: https://join.slack.com/t/votca/signup
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Re: [votca] Regarding using PMF as effective potential.

[Christoph Junghans]

On Sun, Feb 18, 2024 at 10:42 AM 'YUVRAJ SINGH' via votca
 wrote:
>
> Hello,
> I’m working on calculating the Potential of Mean Force (PMF) between two 
> nanoparticles utilizing umbrella sampling. The reaction coordinate being 
> considered is the distance between the center of mass of the nanoparticles.
>
> Now, I intend to utilize this PMF as an effective potential for simulating 
> systems containing multiple nanoparticles using molecular dynamics. 
> Essentially, each nanoparticle will be represented by a sphere, and their 
> interactions will be governed by the effective potential derived from 
> umbrella sampling.
>
> I think VOTCA can be used to generate a tabulated form of potential.
No, we don't have a tools for that in VOTCA, but you could use do a
fit in numpy or gnuplot.

>
> Can anyone help me start this simulation ?
I would just take a box of LJ particles with the right density, change
the potential and start with that.

Christoph

>
>
> Thank you
>
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Re: [votca] problem in building VOTCA

[Christoph Junghans]

On Fri, Feb 16, 2024 at 10:49 AM Roozbeh R  wrote:
>
> Hi Christoph,
> I tried cmake command line:  cmake -B builddir -S votca  
> -DCMAKE_INSTALL_PREFIX=${prefix}  -DINSTALL_CSGAPPS=ON  
> -DBUILD_OWN_GROMACS=ON  -DGMX_EXTRA_CMAKE_ARGS="-DGMX_CUDA_TARGET_SM=90"
>
> and next:
> cmake --build builddir --parallel 10
>
> This time ,at the making stage, it apparently could make GMX with no error , 
> but then a new error message erupts :
>
> "
> [  4%] Linking CXX shared library libvotca_tools.so
> /usr/bin/ld: /usr/local/lib/libfftw3.a(assert.o): warning: relocation against 
> `stdout@@GLIBC_2.2.5' in read-only section `.text'
> /usr/bin/ld: /usr/local/lib/libfftw3.a(assert.o): relocation R_X86_64_PC32 
> against symbol `stdout@@GLIBC_2.2.5' can not be used when making a shared 
> object; recompile with -fPIC
> /usr/bin/ld: final link failed: bad value
> collect2: error: ld returned 1 exit status
> gmake[2]: *** [tools/src/libtools/CMakeFiles/votca_tools.dir/build.make:679: 
> tools/src/libtools/libvotca_tools.so.2024] Error 1
> gmake[1]: *** [CMakeFiles/Makefile2:1564: 
> tools/src/libtools/CMakeFiles/votca_tools.dir/all] Error 2
> gmake: *** [Makefile:146: all] Error 2
> "
>
> it seems like a problem linking against fftw3 library , but as the same 
> library is also used for building gromacs (during the same installation 
> process) it is odd. wondering how to get read of the error? (already tried 
> LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib/libfftw3.a which did not work)
>
> Re. I shall check on running Spack with -verbose flag as you requested and 
> report back the result later.
>
> but for now , do you have any advice on how to resolve the above err?
You have a static libfftw (.a), but VOTCA needs a shared one (.so).
You can disable using FFTW with -DCMAKE_DISABLE_FIND_PACKAGE_FFTW3=ON,
it won't cut down VOTCA functionality much. [Or you could recompile
fftw with --enable-shared.]

Christoph
>
> kind regards,
> roozi
> On Thursday, February 15, 2024 at 9:50:36 PM UTC+3:30 Christoph Junghans 
> wrote:
>>
>> On Thu, Feb 15, 2024 at 9:27 AM Christoph Junghans  wrote:
>> >
>> > On Thu, Feb 15, 2024 at 9:10 AM Christoph Junghans  
>> > wrote:
>> > >
>> > > On Wed, Feb 14, 2024 at 5:20 PM Roozbeh R  wrote:
>> > > >
>> > > > Hi Christoph,
>> > > > thank you for the reply.
>> > > > docker does not work either as i have already tested it for other 
>> > > > packages on my system too without success after lots of trials, so i 
>> > > > rather not go after it again.
>> > > >
>> > > > Re. your question on the failure of Spack , yes it succeeds in 
>> > > > installing the dependencies but fails when building VOTCA itself and 
>> > > > there is no error message. it just took a long a long time showing 
>> > > > "building votca" before it says: KILLED! (tested two times)
>> > > Can you do a spack install --verbose ... to see what went on just
>> > > before it's aborting.
>> > >
>> > > >
>> > > > As for the standard method of installing VOTCA, (cmake -B builddir -S 
>> > > > votca -DCMAKE_INSTALL_PREFIX=${prefix} -DINSTALL_CSGAPPS=ON 
>> > > > -DUSE_CUDA=ON) , i managed to modify libgromacs.cmake to get read of 
>> > > > its earlier complain of not being able to find gmx bin, so now it 
>> > > > obviously is possible for cmake to find the location of gmx executable 
>> > > > binary, but now after i run cmake i get a new error message:
>> > > >
>> > > > "
>> > > > ...
>> > > > Found Threads: TRUE
>> > > > -- Found GROMACS: 2019.6
>> > > > CMake Error at CMakeLists.txt:136 (message):
>> > > > Gromacs library was found, but its headers were not. Make sure you have
>> > > > installed the gromacs-devel package or built gromacs with
>> > > > -DGMX_INSTALL_LEGACY_API=ON"
>> > > >
>> > > > but as i checked DGMX_INSTALL_LEGACY_API=ON option is not supported by 
>> > > > gromacsv2019.6 (which is the last gromacs version supporting tabulated 
>> > > > potentials) so this option is not applicable and also i compiled my 
>> > > > gromacsv2019.6 manually with -DGMXAPI=ON and -DBUILD_SHARED_LIBS=ON 
>> > > > which shall suffice. and i don know what gromacs-devel package even 
>> > > > is?!
>> > >
>> > > CMake is just checking with gmx's

Re: [votca] problem in building VOTCA

[Christoph Junghans]

On Thu, Feb 15, 2024 at 9:27 AM Christoph Junghans  wrote:
>
> On Thu, Feb 15, 2024 at 9:10 AM Christoph Junghans  wrote:
> >
> > On Wed, Feb 14, 2024 at 5:20 PM Roozbeh R  wrote:
> > >
> > > Hi Christoph,
> > > thank you for the reply.
> > > docker does not work either as i have already tested it for other 
> > > packages on my system too without success  after lots of trials, so i 
> > > rather not go after it again.
> > >
> > > Re. your question on the failure of Spack , yes it succeeds in installing 
> > > the dependencies but fails when building VOTCA itself and there is no 
> > > error message. it just took a long a long time showing "building votca" 
> > > before it says: KILLED! (tested two times)
> > Can you do a spack install --verbose ... to see what went on just
> > before it's aborting.
> >
> > >
> > > As for the standard method of installing VOTCA, (cmake -B builddir -S 
> > > votca  -DCMAKE_INSTALL_PREFIX=${prefix} -DINSTALL_CSGAPPS=ON  
> > > -DUSE_CUDA=ON) , i managed to modify  libgromacs.cmake to get read of its 
> > > earlier complain of not being able to find gmx bin, so now it obviously 
> > > is possible for cmake to find the location of gmx executable binary,  but 
> > > now after i run cmake i get a new error message:
> > >
> > > "
> > > ...
> > > Found Threads: TRUE
> > > -- Found GROMACS: 2019.6
> > > CMake Error at CMakeLists.txt:136 (message):
> > >   Gromacs library was found, but its headers were not.  Make sure you have
> > >   installed the gromacs-devel package or built gromacs with
> > >   -DGMX_INSTALL_LEGACY_API=ON"
> > >
> > > but as i checked DGMX_INSTALL_LEGACY_API=ON  option is not  supported by 
> > > gromacsv2019.6 (which is the last gromacs version supporting tabulated 
> > > potentials) so this option is not applicable and also i compiled my 
> > > gromacsv2019.6 manually with -DGMXAPI=ON and -DBUILD_SHARED_LIBS=ON which 
> > > shall suffice. and i don know what gromacs-devel package even is?!
> >
> > CMake is just checking with gmx's version.h exists, see
> > https://github.com/votca/votca/blob/master/CMakeLists.txt#L133
> > Considering you had to modifiy your libgromacs.cmake to find the gmx
> > binary that hints toward an issue in your installation, but let me do
> > a build against gmx-2019.6 myself. (We usually use the "release-2019"
> > branch, which should be the same v2019.6).
Ok I added a build against v2019.6 here:
https://github.com/votca/buildenv/pull/208 +
https://github.com/votca/votca/pull/1109
and it seems to work:
https://github.com/votca/votca/actions/runs/7917977239/job/21615345535?pr=1109

> >
> > >
> > > For the other alternative of making votca to build its own gromacs , i 
> > > tried:
> > > cmake -B builddir -S votca  -DCMAKE_INSTALL_PREFIX=${prefix}  
> > > -DINSTALL_CSGAPPS=ON  -DUSE_CUDA=ON  -GMX_CUDA_TARGET_SM=90  
> > > -DBUILD_OWN_GROMACS=ON
> > >
> > > hoping that -DGMX_CUDA_TARGET_SM=90 flag will enable proper installation 
> > > of gromacs by votca automatically ( it worked when i installed  a 
> > > standalone gromacs2019.6 with cuda support on my machine , so i thought  
> > > it might work in this case too) but cmake just says :
> > >
> > > "CMake Warning:
> > >   Manually-specified variables were not used by the project:
> > >
> > > GMX_CUDA_TARGET_SM
> > > USE_CUDA"
> > >
> > > CMAKE indeed made the makefile with no error, but no wonder when i 
> > > proceed to build the votca , i got the blow error (at the stage of 
> > > gromacs automatic build) :
> > >
> > > " nvcc fatal   : Unsupported gpu architecture 'compute_30'
> > > CMake Error at 
> > > gpu_utilstest_cuda_generated_devicetransfers.cu.o.Release.cmake:220 
> > > (message):
> > >   Error generating
> > >   
> > > /root/builddir/gromacs/src/Gromacs_build-build/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utilstest_cuda.dir//./gpu_utilstest_cuda_generated_devicetransfers.cu.o
> > >  "
> > >
> > > it is not a surprise since it is mandatory to make the gpu structure 
> > > clear through an appropriate cmake flag like GMX_CUDA_TARGET_SM,  for 
> > > building the older versions of gromacs on machines with new GPU 
> > > architecture according to gromacs team.
> > >
> > >
> > > Now I think there shall be some 

Re: [votca] problem in building VOTCA

[Christoph Junghans]

On Thu, Feb 15, 2024 at 9:10 AM Christoph Junghans  wrote:
>
> On Wed, Feb 14, 2024 at 5:20 PM Roozbeh R  wrote:
> >
> > Hi Christoph,
> > thank you for the reply.
> > docker does not work either as i have already tested it for other packages 
> > on my system too without success  after lots of trials, so i rather not go 
> > after it again.
> >
> > Re. your question on the failure of Spack , yes it succeeds in installing 
> > the dependencies but fails when building VOTCA itself and there is no error 
> > message. it just took a long a long time showing "building votca" before it 
> > says: KILLED! (tested two times)
> Can you do a spack install --verbose ... to see what went on just
> before it's aborting.
>
> >
> > As for the standard method of installing VOTCA, (cmake -B builddir -S votca 
> >  -DCMAKE_INSTALL_PREFIX=${prefix} -DINSTALL_CSGAPPS=ON  -DUSE_CUDA=ON) , i 
> > managed to modify  libgromacs.cmake to get read of its earlier complain of 
> > not being able to find gmx bin, so now it obviously is possible for cmake 
> > to find the location of gmx executable binary,  but now after i run cmake i 
> > get a new error message:
> >
> > "
> > ...
> > Found Threads: TRUE
> > -- Found GROMACS: 2019.6
> > CMake Error at CMakeLists.txt:136 (message):
> >   Gromacs library was found, but its headers were not.  Make sure you have
> >   installed the gromacs-devel package or built gromacs with
> >   -DGMX_INSTALL_LEGACY_API=ON"
> >
> > but as i checked DGMX_INSTALL_LEGACY_API=ON  option is not  supported by 
> > gromacsv2019.6 (which is the last gromacs version supporting tabulated 
> > potentials) so this option is not applicable and also i compiled my 
> > gromacsv2019.6 manually with -DGMXAPI=ON and -DBUILD_SHARED_LIBS=ON which 
> > shall suffice. and i don know what gromacs-devel package even is?!
>
> CMake is just checking with gmx's version.h exists, see
> https://github.com/votca/votca/blob/master/CMakeLists.txt#L133
> Considering you had to modifiy your libgromacs.cmake to find the gmx
> binary that hints toward an issue in your installation, but let me do
> a build against gmx-2019.6 myself. (We usually use the "release-2019"
> branch, which should be the same v2019.6).
>
> >
> > For the other alternative of making votca to build its own gromacs , i 
> > tried:
> > cmake -B builddir -S votca  -DCMAKE_INSTALL_PREFIX=${prefix}  
> > -DINSTALL_CSGAPPS=ON  -DUSE_CUDA=ON  -GMX_CUDA_TARGET_SM=90  
> > -DBUILD_OWN_GROMACS=ON
> >
> > hoping that -DGMX_CUDA_TARGET_SM=90 flag will enable proper installation of 
> > gromacs by votca automatically ( it worked when i installed  a standalone 
> > gromacs2019.6 with cuda support on my machine , so i thought  it might work 
> > in this case too) but cmake just says :
> >
> > "CMake Warning:
> >   Manually-specified variables were not used by the project:
> >
> > GMX_CUDA_TARGET_SM
> > USE_CUDA"
> >
> > CMAKE indeed made the makefile with no error, but no wonder when i proceed 
> > to build the votca , i got the blow error (at the stage of gromacs 
> > automatic build) :
> >
> > " nvcc fatal   : Unsupported gpu architecture 'compute_30'
> > CMake Error at 
> > gpu_utilstest_cuda_generated_devicetransfers.cu.o.Release.cmake:220 
> > (message):
> >   Error generating
> >   
> > /root/builddir/gromacs/src/Gromacs_build-build/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utilstest_cuda.dir//./gpu_utilstest_cuda_generated_devicetransfers.cu.o
> >  "
> >
> > it is not a surprise since it is mandatory to make the gpu structure clear 
> > through an appropriate cmake flag like GMX_CUDA_TARGET_SM,  for building 
> > the older versions of gromacs on machines with new GPU architecture 
> > according to gromacs team.
> >
> >
> > Now I think there shall be some subtle easy tuning for cmake to be able to 
> > find the gromacs header files it needs in the standard approach(cmake -B 
> > builddir -S votca  -DCMAKE_INSTALL_PREFIX=${prefix} -DINSTALL_CSGAPPS=ON  
> > -DUSE_CUDA=ON). can you help on how to fix it? i mean which headers cmake 
> > is trying to find and how to guide it to find them? because gromacsv2019.6 
> > is already working smoothly on my machine and i can run it from any folder. 
> > so i do not understand which headers it is missing? kindly please advise.
> >
> > also for the 2nd alternative, if one can give right flags to cmake enabling 
> > votca building its own gromacs , this shall absolv

Re: [votca] problem in building VOTCA

[Christoph Junghans]

On Wed, Feb 14, 2024 at 5:20 PM Roozbeh R  wrote:
>
> Hi Christoph,
> thank you for the reply.
> docker does not work either as i have already tested it for other packages on 
> my system too without success  after lots of trials, so i rather not go after 
> it again.
>
> Re. your question on the failure of Spack , yes it succeeds in installing the 
> dependencies but fails when building VOTCA itself and there is no error 
> message. it just took a long a long time showing "building votca" before it 
> says: KILLED! (tested two times)
Can you do a spack install --verbose ... to see what went on just
before it's aborting.

>
> As for the standard method of installing VOTCA, (cmake -B builddir -S votca  
> -DCMAKE_INSTALL_PREFIX=${prefix} -DINSTALL_CSGAPPS=ON  -DUSE_CUDA=ON) , i 
> managed to modify  libgromacs.cmake to get read of its earlier complain of 
> not being able to find gmx bin, so now it obviously is possible for cmake to 
> find the location of gmx executable binary,  but now after i run cmake i get 
> a new error message:
>
> "
> ...
> Found Threads: TRUE
> -- Found GROMACS: 2019.6
> CMake Error at CMakeLists.txt:136 (message):
>   Gromacs library was found, but its headers were not.  Make sure you have
>   installed the gromacs-devel package or built gromacs with
>   -DGMX_INSTALL_LEGACY_API=ON"
>
> but as i checked DGMX_INSTALL_LEGACY_API=ON  option is not  supported by 
> gromacsv2019.6 (which is the last gromacs version supporting tabulated 
> potentials) so this option is not applicable and also i compiled my 
> gromacsv2019.6 manually with -DGMXAPI=ON and -DBUILD_SHARED_LIBS=ON which 
> shall suffice. and i don know what gromacs-devel package even is?!

CMake is just checking with gmx's version.h exists, see
https://github.com/votca/votca/blob/master/CMakeLists.txt#L133
Considering you had to modifiy your libgromacs.cmake to find the gmx
binary that hints toward an issue in your installation, but let me do
a build against gmx-2019.6 myself. (We usually use the "release-2019"
branch, which should be the same v2019.6).

>
> For the other alternative of making votca to build its own gromacs , i tried:
> cmake -B builddir -S votca  -DCMAKE_INSTALL_PREFIX=${prefix}  
> -DINSTALL_CSGAPPS=ON  -DUSE_CUDA=ON  -GMX_CUDA_TARGET_SM=90  
> -DBUILD_OWN_GROMACS=ON
>
> hoping that -DGMX_CUDA_TARGET_SM=90 flag will enable proper installation of 
> gromacs by votca automatically ( it worked when i installed  a standalone 
> gromacs2019.6 with cuda support on my machine , so i thought  it might work 
> in this case too) but cmake just says :
>
> "CMake Warning:
>   Manually-specified variables were not used by the project:
>
> GMX_CUDA_TARGET_SM
> USE_CUDA"
>
> CMAKE indeed made the makefile with no error, but no wonder when i proceed to 
> build the votca , i got the blow error (at the stage of gromacs automatic 
> build) :
>
> " nvcc fatal   : Unsupported gpu architecture 'compute_30'
> CMake Error at 
> gpu_utilstest_cuda_generated_devicetransfers.cu.o.Release.cmake:220 (message):
>   Error generating
>   
> /root/builddir/gromacs/src/Gromacs_build-build/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utilstest_cuda.dir//./gpu_utilstest_cuda_generated_devicetransfers.cu.o
>  "
>
> it is not a surprise since it is mandatory to make the gpu structure clear 
> through an appropriate cmake flag like GMX_CUDA_TARGET_SM,  for building the 
> older versions of gromacs on machines with new GPU architecture according to 
> gromacs team.
>
>
> Now I think there shall be some subtle easy tuning for cmake to be able to 
> find the gromacs header files it needs in the standard approach(cmake -B 
> builddir -S votca  -DCMAKE_INSTALL_PREFIX=${prefix} -DINSTALL_CSGAPPS=ON  
> -DUSE_CUDA=ON). can you help on how to fix it? i mean which headers cmake is 
> trying to find and how to guide it to find them? because gromacsv2019.6 is 
> already working smoothly on my machine and i can run it from any folder. so i 
> do not understand which headers it is missing? kindly please advise.
>
> also for the 2nd alternative, if one can give right flags to cmake enabling 
> votca building its own gromacs , this shall absolve the issue.so i wonder  
> why -DGMX_CUDA_TARGET_SM=90 does not work?! while it works fine when used as 
> a flag to build gromacsv2019.6 independently. Any idea how to pass this info 
> to cmake?
Well, the GMX_CUDA_TARGET_SM is not handover to internal build. Let me
think about how we could fit that.

Christoph

>
> Any help will be highly appreciated,
> roozi
> On Wednesday, February 14, 2024 at 4:52:12 PM UTC+3:30 Christoph Junghans 
> wrote:
>>
>> On Wed, Feb 14, 2024 at 6:38 AM Roozbeh R 

Re: [votca] problem in building VOTCA

[Christoph Junghans]

On Wed, Feb 14, 2024 at 6:38 AM Roozbeh R  wrote:
>
> Hi,
> I am trying to install votca on WSL2 (a laptop). I have already installed 
> gromacs2018.8 &  added the address of the gromacs bin to the .bashrc PATH 
> variable file and made sure that it runs smoothly.
>
>  I try to compile votca (v2024), using cmake command line :
> "cmake -B builddir -S votca -DBUILD_XTP=ON  -DCMAKE_INSTALL_PREFIX=${prefix}  
> -DBUILD_OWN_LIBINT=ON"
>
> Upon running, i got the following error message:
>
> "
> CMake Error at /usr/local/share/cmake/gromacs/libgromacs.cmake:111 (message):
>   The imported target "Gromacs::gmx" references the file
>
>  "/usr/local/bin/gmx"
This means the installed gromacs is missing the "gmx" binary, you
might want to check where it is located and then fix the location in
the libgromacs.cmake.

>
>   but this file does not exist.  Possible reasons include:
>
>   * The file was deleted, renamed, or moved to another location.
>
>   * An install or uninstall procedure did not complete successfully.
>
>   * The installation package was faulty and contained
>
>  "/usr/local/share/cmake/gromacs/libgromacs.cmake"
>
>   but not all the files it references.
>
> Call Stack (most recent call first):
>   /usr/local/share/cmake/gromacs/gromacs-config.cmake:56 (include)
>   CMakeLists.txt:119 (find_package)
> "
>
> Tried resolving it by passing necessary flag containing gromacs info to 
> cmake, like this:
>
> "cmake -B builddir -S votca -DBUILD_XTP=ON -DCMAKE_INSTALL_PREFIX=${prefix} 
> -DBUILD_OWN_LIBINT=ON  -DGROMACS_INCLUDE_DIR=/usr/local/gromacs2018/include 
> -DGROMACS_LIBRARY=/usr/local/gromacs2018/lib/libgromacs.so"
>
> but got the exact same error message as above.
>
> I then tried using the -DBUILD_OWN_GROMACS=ON  :
>
> "cmake -B builddir -S votca -DBUILD_XTP=ON -DCMAKE_INSTALL_PREFIX=${prefix} 
> -DBUILD_OWN_LIBINT=ON  -DBUILD_OWN_GROMACS=ON"
>
> this time, cmake could produce the makefile with no error, however when i 
> continue further to make the votca (cmake --build builddir --parallel 10), 
> got the following error msg  :
>
> "nvcc fatal   : Unsupported gpu architecture 'compute_30'
> CMake Error at 
> gpu_utilstest_cuda_generated_devicetransfers.cu.o.Release.cmake:220 (message):
>   Error generating
>   
> /root/builddir/gromacs/src/Gromacs_build-build/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utilstest_cuda.dir//./gpu_utilstest_cuda_generated_devicetransfers.cu.o"
>
> which is apparently due to the fact that gromacs version which was to be 
> installed (with -DBUILD_OWN_GROMACS=ON) is way too old (probably v.2019...?) 
> to support the system's gpu architecture : nvidia's RTX-4060. (actually i had 
> to compile my build of the gromacs2018.8 without a gpu support for the same 
> reason.)
That might be more of a gromacs issue, but 2019 is too old for
upstream to fix anything.

>
> as a final resort, i tried building votca with spack (spack install votca).
> apparently, it proceeded successfully to install all the prerequisite 
> packages and dependencies (including gromacs v2019...) right to the final 
> step of building votca package itself, at which point it just took forever to 
> complete and finally spitted out :"KILLED"
When is it getting killed? When building VOTCA? Can you post an error message?

>
> so after testing all options to build VOTCA , to no avail, I am desperate to 
> find a workaround.
> any comment/guidelines  will be highly appreciated!
Have you tried docker? Just get docker for Windows and then run the
votca/votca container.

Christoph

>
> Thanks!
> Roozi
>
>
>
>
>
>
> --
> Join us on Slack: https://join.slack.com/t/votca/signup
> ---
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> To unsubscribe from this group and stop receiving emails from it, send an 
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> To view this discussion on the web visit 
> https://groups.google.com/d/msgid/votca/d49cd700-a1da-4df7-9962-4244cb4004dbn%40googlegroups.com.



-- 
Christoph Junghans
Web: http://www.compphys.de

-- 
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Re: [votca] Mapping Block-copolymer

[Christoph Junghans]

On Sun, Feb 4, 2024 at 9:47 AM Pratyasha Bhardwaj
 wrote:
>
> Dear Christoph,
>
> Thank you for the quick reply. What I meant is I have a gro file where the PE 
> molecules are named as PEX , PEY and so on, each having different length and 
> then I have PEG molecule. I have bonds between the different PE and PEG 
> chains forming a large copolymer chain. If I define one mapping file per 
> molecule, how will I account for the bonds between these different molecules.

Votca doesn't support bonds between different molecules, but you can
also map the PE* parts separately and then reintroduce the bonds in
the coarse-grained topology by hand.

Christoph

>
> Thank you
> Pratyasha
>
>
> On Sunday, February 4, 2024 at 9:07:35 PM UTC+5:30 Christoph Junghans wrote:
>>
>> On Sun, Feb 4, 2024 at 8:16 AM Pratyasha Bhardwaj
>>  wrote:
>> >
>> > Dear Users,
>> >
>> > How do I map a block copolymer in votca? My all-atom system has PE- PEG 
>> > copolymer chains and water. Since PE and PEG are bonded to each other , 
>> > how do I define the mapping file?
>> See here: https://www.votca.org/csg/input_files.html#mapping-files
>>
>> > What do I put in the 'ident' tag in the xml file.
>> It is the name of the molecule from the topology file.
>>
>> > Could you please help me out?
>> You could try to use Stock as well: http://stock.cmm.ki.si/smt/
>>
>> Christoph
>> >
>> > Thank You
>> > Pratyasha
>> >
>> > --
>> > Join us on Slack: https://join.slack.com/t/votca/signup
>> > ---
>> > You received this message because you are subscribed to the Google Groups 
>> > "votca" group.
>> > To unsubscribe from this group and stop receiving emails from it, send an 
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>>
>>
>>
>> --
>> Christoph Junghans
>> Web: http://www.compphys.de
>
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Re: [votca] Mapping Block-copolymer

[Christoph Junghans]

On Sun, Feb 4, 2024 at 8:16 AM Pratyasha Bhardwaj
 wrote:
>
> Dear Users,
>
> How do I map a block copolymer in votca? My all-atom system has PE- PEG 
> copolymer chains and water. Since PE and PEG are bonded to each other , how 
> do I define the mapping file?
See here: https://www.votca.org/csg/input_files.html#mapping-files

> What do I put in the 'ident' tag in the xml file.
It is the name of the molecule from the topology file.

> Could you please help me out?
You could try to use Stock as well: http://stock.cmm.ki.si/smt/

Christoph
>
> Thank You
> Pratyasha
>
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Re: [votca] How to use steepest decent in re minimization?

[Christoph Junghans]

On Wed, Jan 24, 2024 at 8:52 AM dd ding  wrote:
>
> Hello, may I ask if the deepest method in votca2024 can now be applied?
Not sure, do you mean steepest descent method? If so you can only use
that in the prepare step for each iteration, but not the iteration run
itself.
I guess you could force VOTCA to use it for the normal iteration as
well, but that would not be NVT ensemble anymore.

 If cg. inverse. re. do is set in XML_ Step, an error message will
appear stating "The settings XML file contains the tags which do not
exist in the XML defaults file:
> ./inverse/re/do_ Step. May I ask what the reason is?
Since VOTCA 2023, we check a bit more aggressively for unknown
options, to help the users with typos.
I think you mean the option , and a couple of postadd
scripts have a  option as well.

> Also, I would like to ask, after setting "Hessian check=false", does the 
> Newton method not detect whether the Hessian matrix is positive definite, or 
> is it not using the Newton method at this point?
By default the csg_reupdate / the relative entropy method checks with
the Hessian is positive definite, but for development purposes we have
an option to disable that check, but you cannot get to it easily
outside the testing framework, i.e. there is no option in the XML file
to disable it.

Hope that helps,

Christoph

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[votca] Votca 2024 released

[Christoph Junghans]

Dear all,

Votca 2024 was just released.

As the 2023 release was so late, this release only has very few fixes
mostly in the xtp module. A
detailed list of changes can be found here:
https://github.com/votca/votca/blob/master/CHANGELOG.rst

Thanks to everyone who contributed features for this release!
Details can be found here:
https://github.com/votca/votca/graphs/contributors

As usual due to a lack of developers we will NOT fix any bugs in the
previous Votca releases (2023.X and below) anymore, so we encourage
everyone to update and use the new version.

Fedora, OpenSuse and Spack packages are on their way.

Cheers,

Christoph

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Re: [votca] Topology does not have beads of type "A"

[Christoph Junghans]

r of beads in trajectory do not match topology
>>>>> "
>>>>> My top file is still the email from Creep
>>>>> [image: 微信图片_20231128205415.png]
>>>>> 在2023年11月28日星期二 UTC+8 03:36:14 写道：
>>>>>
>>>>>> On Mon, Nov 27, 2023 at 7:30 AM shu zong  wrote:
>>>>>>
>>>>>>> Dear teacher, hello. I was calculating the propane example, and I
>>>>>>> ran into a problem. The "Topology does not have beads of type "A" "error
>>>>>>> occurs when calculating the RDF of the objective function. Please help 
>>>>>>> me
>>>>>>> to see if there is something wrong with the xml and top files
>>>>>>> [image: 微信图片_20231127222044.png][image: 微信图片_20231127222126.png][image:
>>>>>>> 微信图片_2023112704.png]
>>>>>>
>>>>>> I think you are mixing two things up!
>>>>>>
>>>>>> Your gromacs topology is at the coarse-grained level, but your
>>>>>> mapping file is for the atomistic level.
>>>>>>
>>>>>> An example for everything atomistic can be found here:
>>>>>>
>>>>>> https://github.com/votca/votca/tree/master/csg-tutorials/propane/atomistic
>>>>>>
>>>>>> an example for everything coarse-grained is here:
>>>>>> https://github.com/votca/votca/tree/master/csg-tutorials/propane/ibi
>>>>>>
>>>>>> Christoph
>>>>>>
>>>>>> PS: please do NOT put screenshots in the email, they are not
>>>>>> searchable and hence won't be very useful for other users with a similar
>>>>>> issue.
>>>>>> Instead, attach the input files and copy error messages into the
>>>>>> email directly.
>>>>>>
>>>>>> --
>>>>>>
>>>>>>> Join us on Slack: https://join.slack.com/t/votca/signup
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>>>>>>> .
>>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Christoph Junghans
>>>>>> Web: http://www.compphys.de
>>>>>>
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>>>>>
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>>>>> .
>>>>>
>>>>
>>>>
>>>> --
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>>>> Web: http://www.compphys.de
>>>>
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>>> .
>>>
>>
>>
>> --
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>> Web: http://www.compphys.de
>>
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Re: [votca] Topology does not have beads of type "A"

[Christoph Junghans]

On Thu, Nov 30, 2023 at 12:48 AM shu zong  wrote:

>
> Thank you very much for your reply. The first email I sent was with this
> command, "csg_stat --top topol.tpr --trj traj.trr --cg propane.xml
> --options settings.xml." However, the "Topology does not have beads of type
> "A" "error is displayed。
>
> I'm using this example.
>  an example for everything coarse-grained is here:
> https://github.com/votca/votca/tree/master/csg-tutorials/propane/ibi
>
> test/ibi$ csg_stat --top topol.tpr --trj traj.trr --cg propane.xml
> --options settings.xml
>
This is an IBI tutorial, which is already on the coarse-grained level hence
you don't need to specify a mapping file (--cg option) as there is nothing
to map.
To run IBI just use csg_inverse (see run.sh).

See this tutorial on how to do IBI:
https://www.votca.org/csg-tutorials/Tutorial.html#iterative-boltzmann-inversion-ibi-for-spc-e-water

Christoph



>
> begin to calculate distribution functions
> # of bonded interactions: 0
> # of non-bonded interactions: 3
> Reading file topol.tpr, VERSION 2020.1 (single precision)
> I have 11000 beads in 1000 molecules
> I have 3000 beads in 1000 molecules for the coarsegraining
> trr version: GMX_trn_file (single precision)
> Reading frame   0 time0.000
> an error occurred:
> Topology does not have beads of type "A"
> This was specified in type1 of interaction "A-A"
> xuqch@chasing:~/simulation/Xuqch/test/ibi$
>
> 在2023年11月29日星期三 UTC+8 00:18:22 写道：
>
>> On Tue, Nov 28, 2023 at 5:56 AM shu zong  wrote:
>>
>>> Thank you very much for your reply.
>>> Through the teacher's explanation, I realized my mistake. The command I
>>> used earlier was "csg_stat --top topol.tpr --trj traj.trr --cg propane.xml
>>> --options settings.xml", Among them, topol.tpr and traj.trr are atomic
>>> files.
>>>  Now I convert the trace file traj.trr with the command "csg_map --top
>>> topol.tpr --trj traj.trr --cg propane.xml --out traj_cg.trr".
>>> But when I use "csg_stat --top topol.tpr --trj traj_cg.trr --cg
>>> propane.xml --options settings.xml" again, I still say that the top file is
>>> faulty.
>>>
>> With a mapping file, please use the atomistic topology and trajectory
>> here, e.g.:
>> $ csg_stat --top topol.tpr --trj traj.trr --cg propane.xml --options
>> settings.xml
>>
>> Christoph
>>
>>>
>>> The problem is "to begin to calculate distribution functions
>>> # of bonded interactions: 0
>>> # of non-bonded interactions: 3
>>> Reading file topol.tpr, VERSION 2020.1 (single precision)
>>> I have 11000 beads in 1000 molecules
>>> I have 3000 beads in 1000 molecules for the coarsegraining
>>> trr version: GMX_trn_file (double precision)
>>> Reading frame 0 time 0.000
>>> an error occurred:
>>> number of beads in trajectory do not match topology
>>> "
>>> My top file is still the email from Creep
>>> [image: 微信图片_20231128205415.png]
>>> 在2023年11月28日星期二 UTC+8 03:36:14 写道：
>>>
>>>> On Mon, Nov 27, 2023 at 7:30 AM shu zong  wrote:
>>>>
>>>>> Dear teacher, hello. I was calculating the propane example, and I ran
>>>>> into a problem. The "Topology does not have beads of type "A" "error 
>>>>> occurs
>>>>> when calculating the RDF of the objective function. Please help me to see
>>>>> if there is something wrong with the xml and top files
>>>>> [image: 微信图片_20231127222044.png][image: 微信图片_20231127222126.png][image:
>>>>> 微信图片_2023112704.png]
>>>>
>>>> I think you are mixing two things up!
>>>>
>>>> Your gromacs topology is at the coarse-grained level, but your mapping
>>>> file is for the atomistic level.
>>>>
>>>> An example for everything atomistic can be found here:
>>>>
>>>> https://github.com/votca/votca/tree/master/csg-tutorials/propane/atomistic
>>>>
>>>> an example for everything coarse-grained is here:
>>>> https://github.com/votca/votca/tree/master/csg-tutorials/propane/ibi
>>>>
>>>> Christoph
>>>>
>>>> PS: please do NOT put screenshots in the email, they are not searchable
>>>> and hence won't be very useful for other users with a similar issue.
>>>> Instead, attach the input files and copy error messages into the email
>>>> directly.
>>>>
>>>> --
>>>>
>&g

Re: [votca] Topology does not have beads of type "A"

[Christoph Junghans]

On Tue, Nov 28, 2023 at 5:56 AM shu zong  wrote:

> Thank you very much for your reply.
> Through the teacher's explanation, I realized my mistake. The command I
> used earlier was "csg_stat --top topol.tpr --trj traj.trr --cg propane.xml
> --options settings.xml", Among them, topol.tpr and traj.trr are atomic
> files.
>  Now I convert the trace file traj.trr with the command "csg_map --top
> topol.tpr --trj traj.trr --cg propane.xml --out traj_cg.trr".
> But when I use "csg_stat --top topol.tpr --trj traj_cg.trr --cg
> propane.xml --options settings.xml" again, I still say that the top file is
> faulty.
>
With a mapping file, please use the atomistic topology and trajectory here,
e.g.:
$ csg_stat --top topol.tpr --trj traj.trr --cg propane.xml --options
settings.xml

Christoph

>
> The problem is "to begin to calculate distribution functions
> # of bonded interactions: 0
> # of non-bonded interactions: 3
> Reading file topol.tpr, VERSION 2020.1 (single precision)
> I have 11000 beads in 1000 molecules
> I have 3000 beads in 1000 molecules for the coarsegraining
> trr version: GMX_trn_file (double precision)
> Reading frame 0 time 0.000
> an error occurred:
> number of beads in trajectory do not match topology
> "
> My top file is still the email from Creep
> [image: 微信图片_20231128205415.png]
> 在2023年11月28日星期二 UTC+8 03:36:14 写道：
>
>> On Mon, Nov 27, 2023 at 7:30 AM shu zong  wrote:
>>
>>> Dear teacher, hello. I was calculating the propane example, and I ran
>>> into a problem. The "Topology does not have beads of type "A" "error occurs
>>> when calculating the RDF of the objective function. Please help me to see
>>> if there is something wrong with the xml and top files
>>> [image: 微信图片_20231127222044.png][image: 微信图片_20231127222126.png][image:
>>> 微信图片_2023112704.png]
>>
>> I think you are mixing two things up!
>>
>> Your gromacs topology is at the coarse-grained level, but your mapping
>> file is for the atomistic level.
>>
>> An example for everything atomistic can be found here:
>> https://github.com/votca/votca/tree/master/csg-tutorials/propane/atomistic
>>
>> an example for everything coarse-grained is here:
>> https://github.com/votca/votca/tree/master/csg-tutorials/propane/ibi
>>
>> Christoph
>>
>> PS: please do NOT put screenshots in the email, they are not searchable
>> and hence won't be very useful for other users with a similar issue.
>> Instead, attach the input files and copy error messages into the email
>> directly.
>>
>> --
>>
>>> Join us on Slack: https://join.slack.com/t/votca/signup
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>>> .
>>>
>>
>>
>> --
>> Christoph Junghans
>> Web: http://www.compphys.de
>>
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[votca] Votca 2023 released

[Christoph Junghans]

Dear all,

Better late than never: Votca 2023 was just released.

The release is packed with new features, mostly in the xtp module. A
detailed list of changes can be found here:
https://github.com/votca/votca/blob/master/CHANGELOG.rst

Thanks to everyone who contributed features for this release!
Details can be found here:
https://github.com/votca/votca/graphs/contributors

As usual due to a lack of developers we will NOT fix any bugs in the
previous Votca releases (2022.X and below) anymore, so we encourage
everyone to update and use the new version.

Fedora, OpenSuse and Spack packages are on their way.

Cheers,

Christoph

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Re: [votca] Ask questions

[Christoph Junghans]

On Wed, Nov 8, 2023 at 1:40 AM shu zong  wrote:

> Hello teacher, I just learned OVTCA recently.
> I would like to know what is the basis for the setting of these three
> parameters in the propane example? Was it random?[image:
> 微信图片_20231108163959.png]
>

It is the range of RDF you want to invert.

I would suggest to do the tutorial here first:

https://www.votca.org/csg-tutorials/Tutorial.html#iterative-boltzmann-inversion-ibi-for-spc-e-water

Christoph

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Re: [votca] reading tpx file (topol.tpr) version 122 with version 119 program

[Christoph Junghans]

On Thu, Nov 2, 2023 at 5:43 AM shu zong  wrote:

> Thank you very much for your reply. Through your guidance, I have solved
> the problem[image: 微信图片_20231102194314.png]
>
On a related note, Gromacs-2020 and newer don't support tabulated
interactions, so if you want to do IBI and such you will have to use
gromacs-2019 anyhow.

Christoph

>
> 在2023年11月2日星期四 UTC+8 12:22:25 写道：
>
>> b
>>
>> On Wed, Nov 1, 2023 at 9:03 PM shu zong  wrote:
>>
>>> I have installed gmx and VOTCA. When I go to calculate the example,
>>> there is always an error, is it my GMX version? How do I operate
>>
>> [image: 微信图片_20231102110144.png]
>>>
>>> The error basically means the tpr file was made with a newer version of
>> gromacs (2021.2) than VOTCA is using (2020.1).
>> You will either have to use the older version of gromacs to make the tpr
>> or recompile VOTCA to use the newer version of gromacs.
>>
>> Christoph
>>
>>
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>>
>>
>> --
>> Christoph Junghans
>> Web: http://www.compphys.de
>>
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Re: [votca] reading tpx file (topol.tpr) version 122 with version 119 program

[Christoph Junghans]

b

On Wed, Nov 1, 2023 at 9:03 PM shu zong  wrote:

> I have installed gmx and VOTCA. When I go to calculate the example, there
> is always an error, is it my GMX version? How do I operate

[image: 微信图片_20231102110144.png]
>
> The error basically means the tpr file was made with a newer version of
gromacs (2021.2) than VOTCA is using (2020.1).
You will either have to use the older version of gromacs to make the tpr or
recompile VOTCA to use the newer version of gromacs.

Christoph


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Re: [votca] mapping two different molecules for ibi

[Christoph Junghans]

On Wed, Sep 27, 2023 at 6:55 AM Saeed Norouzi  wrote:
>
> Dear Christoph,
>
> Thank you for your help. I made two map files and now I have the target 
> distributions. Now, I am trying to do the iteration part and I have an error 
> again on the mapping part. I build two CG mapping files 
> (CG-CG-mapping-polymer.xml;CG-CG-mapping-particle.xml) for polymer and 
> particle. Also, in the setting file I have specified those two by 
> CG-CG-mapping-polymer.xml;CG-CG-mapping-particle.xml/
>
> So far everything seems fine to me, but there is an error regarding bonded 
> interaction that I cannot fix. I only have 3 non-bond potentials which need 
> to be matched with the target, and I have no idea what it means for bonded 
> interaction.
>
> I attached the setting file, map files for CG, log file and also my CG 
> trajectory file here.
>
> I would really appreciate your help with this.
First of all if you don't plan to do IBI on the bonded interaction,
you won't need a mapping file.

The error hints at a typo in the mapping file.
I would run
$ csg_dump -top CG-topolgy.xml --cg
/data/snorouzi/data/3-PLA/ibi_PLA/nano_particle/"CG-CG-mapping-particle.xml;CG-CG-mapping-polymer.xml
to see what VOTCA reads.

Christoph

>
> PS: I also tried this command (csg_stat --nt 24 --options 
> /data/snorouzi/data/3-PLA/ibi_PLA/nano_particle/settings.xml --top 
> CG-topolgy.xml --trj traj.dump --begin 0 --first-frame 0 --cg 
> /data/snorouzi/data/3-PLA/ibi_PLA/nano_particle/"CG-CG-mapping-particle.xml;CG-CG-mapping-polymer.xml")
>   the error is "cannot find: <109> in DEOAA an error occurred: error while 
> trying to create bonded interaction, bead 109 not found" which still I could 
> not see what it means by  creating bonded interaction.
>
>
> 
> # 
>  #
> # ERROR:  
>  #
> # calc_rdf_generic.sh: Mapping file 
> 'CG-CG-mapping-polymer.xml;CG-CG-mapping-particle.xml' for bonded interaction 
> not found in maindir #
> # For details see the logfile 
> /data/snorouzi/data/3-PLA/ibi_PLA/nano_particle/inverse.log   
>#
> # 
>  #
> 
> die: (called from 11538)  CSG_MASTER_PID is 7773
> die: pids to kill:  7773 11417 11523 11538
>
>
> Best regards
> Saeed
>
>
> On Fri, Sep 22, 2023 at 7:03 PM Christoph Junghans  wrote:
>>
>> On Fri, Sep 22, 2023 at 3:09 AM Saeed Norouzi  wrote:
>> >
>> > Dear Christoph and votca users,
>> >
>> >
>> > I am trying to do a CG model for my polymer system and nanoparticle. The 
>> > CG model for the pure polymer is done using ibi. Now I need to find the 
>> > interaction between the nanoparticle and polymer (do ibi for non-bond 
>> > interaction between the particle beads and polymer). I have created the 
>> > all-atom topology and mapping file for the polymer (molecule name is DEOAA 
>> > in .xml file) and also for the nanoparticle (molecule name is particle in 
>> > the .xml file). csg_map command (csg_map --top AA-topology.xml --trj 
>> > no_bpc.xtc --out traj-CG.dump --cg A2Cmapping.xml ) runs successfully, but 
>> > the problem is that the CG trajectory does not include the nanoparticle 
>> > structure (only shows the polymer which is type A B C). My particles also 
>> > have three types P4 P5 P6.
>> > PS: the particle is mapped to 104 beads and each polymer chain includes 13 
>> > beads.
>> > I have attached the topology and mapping file here. I appreciate your help.
>> For two molecules you will need to call csg_map with two mapping
>> files, e.g. csg_map  --cg "map1.xml;map2.xml".
>>
>> Christoph
>>
>> >
>> > Best regards
>> > saeed
>> >
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Re: [votca] mapping two different molecules for ibi

[Christoph Junghans]

On Fri, Sep 22, 2023 at 3:09 AM Saeed Norouzi  wrote:
>
> Dear Christoph and votca users,
>
>
> I am trying to do a CG model for my polymer system and nanoparticle. The CG 
> model for the pure polymer is done using ibi. Now I need to find the 
> interaction between the nanoparticle and polymer (do ibi for non-bond 
> interaction between the particle beads and polymer). I have created the 
> all-atom topology and mapping file for the polymer (molecule name is DEOAA in 
> .xml file) and also for the nanoparticle (molecule name is particle in the 
> .xml file). csg_map command (csg_map --top AA-topology.xml --trj no_bpc.xtc 
> --out traj-CG.dump --cg A2Cmapping.xml ) runs successfully, but the problem 
> is that the CG trajectory does not include the nanoparticle structure (only 
> shows the polymer which is type A B C). My particles also have three types P4 
> P5 P6.
> PS: the particle is mapped to 104 beads and each polymer chain includes 13 
> beads.
> I have attached the topology and mapping file here. I appreciate your help.
For two molecules you will need to call csg_map with two mapping
files, e.g. csg_map  --cg "map1.xml;map2.xml".

Christoph

>
> Best regards
> saeed
>
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Re: [votca] Topology does not have beads of type, which was specified in type1 of interaction "*-*"

[Christoph Junghans]

On Mon, Sep 11, 2023 at 10:04 AM Ran Zhao  wrote:

> Dear all:
>
>I am currently using VOTCA to do an IBI process for a single
> polymer based on a dataset obtained from the experiments and utilizing
> LAMMPS to perform molecular dynamic simulations.
>
>After all the preparations, VOTCA successfully performed the
> first step of the iterative Boltzmann inversion. But when VOTCA is ready to
> start the second step of the inversion, there is an error when using the
> csg_stat command to invert the non-bonded potential, As shown in the figure
> below.
> [image: e_1.png]
>
> I then realized that I didn't give the atom types special character names
> in the LAMMPS topology file (lammps.data). As far as I know, it doesn't
> seem to be possible to name atom types by a string in LAMMPS topology file.
>
> I refer to the example given in csg-tutorial file (spce water:
> ibi_lammps), the atom type of CG water beads in the topology file is "1",
> and there is Bead1  in settings.xml. I also changed this to
> Bead1 in my settings.xml file, but there is still an error!
> [image: e_2.png]
> Then, I just write "1" in the settings.xml file, but this error still
> exists.
>
> I've been plagued by this error for days. Hopefully, I can get some help
> from you!
>
You can just run "csg_dump --top " to see what votca
reads. If the lammps topology doesn't work for you, you can alternatively
create an xml topology file.

Christoph


> Yours sincerely
> Boran Zhao
>
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Re: [votca] When doing an IbI process conbining with LAMMPS, can I use LJ units in lammps?

[Christoph Junghans]

On Tue, Sep 5, 2023 at 8:25 PM Ran Zhao  wrote:
>
> Dear all:
>
> As discussed in VOTCA manual, VOTCA requires all input and output files to be 
> in scaled units. Scaled units are a way of expressing the physical quantities 
> in a dimensionless form.
Sorry, where in the manual does it say that?

>
> However, my research topic requires using unscaled units, so I must set units 
> to lj in lammps.in files.
>
> Can I  tell VOTCA to use dimensionless units to calculate potentials and 
> iterate them?
VOTCA thinks it reads AA from the lammps trajectory file and then writes nm.
But of course, you can trick it into reading in any units, you will
just have to scale the output accordingly.

Christoph
>
> Best,
> Boran Zhao
>
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Re: [votca] units in votca

[Christoph Junghans]

On Fri, Aug 18, 2023 at 8:39 AM Cecília Álvares 
wrote:

> So the red and black curves were both calculated using csg_stat? If both
> curves (the red and black) are an output of the csg_stat, I dont see how it
> is possible that the curves have different areas underneath them (I would
> say there should be no normalization factor to be applied in this case).
> Your plot made me think of a scenario where you are calculating a
> reference by means of some python code and you are calculating *bond
> distribution functions* and not *probability density functions* for the
> bond (they are not the same). So this is not the case?
>

I think what Ceillia is asking is if you used csg_stat to also calculate
the target distribution.

Additionally a quick back of the envelope calculation:
the IBI update is
delta_U ~= log(d/d_target) =
log(d/(d'_target*Norm))=log(d/d'_target)-log(Norm)
so the Norm will just show up as constant in the potential update and hence
no actual force.

So it doesn't matter for the update, but it will matter for the
convergence number.

Christoph


>
> Em sexta-feira, 18 de agosto de 2023 às 16:03:30 UTC+2, Saeed Norouzi
> escreveu:
>
>> Dear Christoph,
>>
>> Yes, csg_stat using votca for the distribution. I did not touch the angle
>> and dihedrals. just changed the nm to A for the bond and RDF.
>>
>> Best regards
>> Saeed
>>
>> On Fri, Aug 18, 2023 at 3:53 PM Christoph Junghans 
>> wrote:
>>
>>>
>>>
>>> On Fri, Aug 18, 2023 at 7:37 AM Saeed Norouzi 
>>> wrote:
>>>
>>>> Dear all,
>>>>
>>>> I am currently working on my CG ibi using VOTCA. The all-atom
>>>> simulation has been conducted using GROMACS, and I have obtained the target
>>>> distribution from my AA model. For the ibi part, I am utilizing LAMMPS,
>>>> which requires a conversion of units. I achieved this by scaling the bond
>>>> lengths(nm to A) and nonbonded table values (nm to A) by a factor of 10
>>>> using a Python script.
>>>>
>>>> As far as my understanding goes, the populations are unitless, and
>>>> therefore, I believe I do not need to alter the population size. Up to this
>>>> point, the radial distribution function (RDF) appears satisfactory.
>>>> However, I have encountered an issue with the bond distribution from ibi
>>>> iterations not matching the target distribution (please refer to the
>>>> attached image where the red line represents the target distribution, and
>>>> the black line depicts the calculated distribution from ibi iterations).
>>>>
>>>> My question is: Should I also divide the populations for bonds by a
>>>> factor of 10 to ensure consistency?
>>>>
>>> Did you calculate the target distributions with VOTCA as well?
>>> (with csg_stat)
>>> I have to look at the code again, but I believe VOTCA is normalizing the
>>> distribution by some means.
>>>
>>> Christoph
>>>
>>>> Thank you for your assistance.
>>>> [image: Screenshot from 2023-08-18 15-37-12.png]
>>>>
>>>>
>>>> Best regards
>>>>
>>>> Seed
>>>>
>>>> --
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>>>> an email to votca+un...@googlegroups.com.
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>>>> .
>>>>
>>>
>>>
>>> --
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>>> Web: http://www.compphys.de
>>>
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>>> <htt

Re: [votca] units in votca

[Christoph Junghans]

On Fri, Aug 18, 2023 at 7:37 AM Saeed Norouzi  wrote:

> Dear all,
>
> I am currently working on my CG ibi using VOTCA. The all-atom simulation
> has been conducted using GROMACS, and I have obtained the target
> distribution from my AA model. For the ibi part, I am utilizing LAMMPS,
> which requires a conversion of units. I achieved this by scaling the bond
> lengths(nm to A) and nonbonded table values (nm to A) by a factor of 10
> using a Python script.
>
> As far as my understanding goes, the populations are unitless, and
> therefore, I believe I do not need to alter the population size. Up to this
> point, the radial distribution function (RDF) appears satisfactory.
> However, I have encountered an issue with the bond distribution from ibi
> iterations not matching the target distribution (please refer to the
> attached image where the red line represents the target distribution, and
> the black line depicts the calculated distribution from ibi iterations).
>
> My question is: Should I also divide the populations for bonds by a factor
> of 10 to ensure consistency?
>
Did you calculate the target distributions with VOTCA as well?
(with csg_stat)
I have to look at the code again, but I believe VOTCA is normalizing the
distribution by some means.

Christoph

> Thank you for your assistance.
> [image: Screenshot from 2023-08-18 15-37-12.png]
>
>
> Best regards
>
> Seed
>
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> .
>


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Re: [votca] Problem with extrapolation for bonds

[Christoph Junghans]

On Thu, Aug 10, 2023 at 8:21 AM Saeed Norouzi  wrote:

> Dear Christoph,
>
> I just changed the python3 to python3.10 in the check_csg_xml.py script
> and it's working fine.
>
That works, too, just make sure to do the same for all other python scripts
as well.

Christoph

>
> Thanks for the help,
>
>
> On Thu, Aug 10, 2023 at 3:52 PM Christoph Junghans 
> wrote:
>
>>
>>
>> On Thu, Aug 10, 2023 at 2:45 AM Saeed Norouzi 
>> wrote:
>>
>>> Dear Christoph,
>>>
>>> The problem was with the boots package on my machine. I turned off the
>>> DBUILD_MANPAGES, and the installation was successful, however, I cannot run
>>> my setting file for the same python error(below is the error from
>>> inverse.log).
>>> I think this is the same problem with DBUILD_MANPAGES, and my VOTCA is
>>> using python2.7 (the default version from the machine). How can I
>>> introduce the new version for python?  I already tried to change the
>>> version using (-DPYTHON_EXECUTABLE:FILEPATH=/usr/local/bin/python3.10) but
>>> did not word.
>>>
>>> cmake -B builddir -S votca -DBUILD_XTP=OFF -DBUILD_MANPAGES=OFF \
>>> -DCMAKE_INSTALL_PREFIX=${prefix} -DBoost_NO_BOOST_CMAKE=TRUE \
>>> -DBoost_NO_SYSTEM_PATHS=TRUE
>>> -DBOOST_ROOT:PATHNAME=/home/snorouzi/programs/boost_1_82_0 \
>>> -DBoost_LIBRARY_DIRS:STRING=/home/snorouzi/programs/boost_1_82_0/stage/lib
>>> \
>>> -DBoost_INCLUDE_DIRS:PATH=/home/snorouzi/programs/boost_1_82_0 \
>>> -DPYTHON_EXECUTABLE:FILEPATH=/usr/local/bin/python3.10
>>>
>>>
>>>
>>>
>>>
>>> csg_get_property: returning emtpy value for
>>> 'cg.non-bonded.inverse.imc.reg'
>>> Running subscript 'check_csg_xml.py
>>> /data/snorouzi/data/ibi_PLA/VOTCA_newversion/settings.xml
>>> /home/snorouzi/programs/VOTCA/installdir/share/votca/xml/csg_defaults.xml'
>>> (from tags check csg_xml) dir
>>> /home/snorouzi/programs/VOTCA/installdir/share/votca/scripts/inverse
>>>   File
>>> "/home/snorouzi/programs/VOTCA/installdir/share/votca/scripts/inverse/check_csg_xml.py",
>>> line 76
>>> child_path = f"{path}/{child.tag}"
>>>
>> This is a bit strange as check_csg_xml.py explicitly calls for python3:
>>
>> https://github.com/votca/votca/blob/master/csg/share/scripts/inverse/check_csg_xml.py#L1
>> Anyhow as a workaround just make there is a python3 in your path that
>> points to your /usr/local/bin/python3.10.
>> E.g.
>> echo $PATH # pick a path
>> cd /home/christoph/.local/bin # e.g. this one
>> ln -s /usr/local/bin/python3.10 python3 # link it.
>>
>> Christoph
>>
>>  ^
>>> SyntaxError: invalid syntax
>>>
>>> Callstack:
>>> /home/snorouzi/programs/VOTCA/installdir/share/votca/scripts/inverse/inverse.sh
>>> - linenumber 111
>>> do_external - linenumber 183 in
>>> /home/snorouzi/programs/VOTCA/installdir/share/votca/scripts/inverse/functions_common.sh
>>>
>>>
>>> On Wed, Aug 9, 2023 at 8:35 PM Christoph Junghans 
>>> wrote:
>>>
>>>>
>>>>
>>>> On Wed, Aug 9, 2023 at 10:31 AM Saeed Norouzi 
>>>> wrote:
>>>>
>>>>> Dear  Christoph,
>>>>>
>>>>> I am trying to install the new version, but there is an error with cmake
>>>>> --build builddir.
>>>>>
>>>>> [ 10%] Building CXX object
>>>>> tools/src/libtools/CMakeFiles/votca_tools.dir/optionshandler.cc.o
>>>>> [ 11%] Building CXX object
>>>>> tools/src/libtools/CMakeFiles/votca_tools.dir/property.cc.o
>>>>> [ 11%] Building CXX object
>>>>> tools/src/libtools/CMakeFiles/votca_tools.dir/propertyiomanipulator.cc.o
>>>>> [ 12%] Building CXX object
>>>>> tools/src/libtools/CMakeFiles/votca_tools.dir/rangeparser.cc.o
>>>>> [ 12%] Building CXX object
>>>>> tools/src/libtools/CMakeFiles/votca_tools.dir/reducededge.cc.o
>>>>> [ 12%] Building CXX object
>>>>> tools/src/libtools/CMakeFiles/votca_tools.dir/reducedgraph.cc.o
>>>>> [ 13%] Building CXX object
>>>>> tools/src/libtools/CMakeFiles/votca_tools.dir/spline.cc.o
>>>>> [ 13%] Building CXX object
>>>>> tools/src/libtools/CMakeFiles/votca_tools.dir/table.cc.o
>>>>> [ 13%] Building CXX object
>>>>> tools/src/libtoo

Re: [votca] Problem with extrapolation for bonds

[Christoph Junghans]

On Thu, Aug 10, 2023 at 2:45 AM Saeed Norouzi  wrote:

> Dear Christoph,
>
> The problem was with the boots package on my machine. I turned off the
> DBUILD_MANPAGES, and the installation was successful, however, I cannot run
> my setting file for the same python error(below is the error from
> inverse.log).
> I think this is the same problem with DBUILD_MANPAGES, and my VOTCA is
> using python2.7 (the default version from the machine). How can I
> introduce the new version for python?  I already tried to change the
> version using (-DPYTHON_EXECUTABLE:FILEPATH=/usr/local/bin/python3.10) but
> did not word.
>
> cmake -B builddir -S votca -DBUILD_XTP=OFF -DBUILD_MANPAGES=OFF \
> -DCMAKE_INSTALL_PREFIX=${prefix} -DBoost_NO_BOOST_CMAKE=TRUE \
> -DBoost_NO_SYSTEM_PATHS=TRUE
> -DBOOST_ROOT:PATHNAME=/home/snorouzi/programs/boost_1_82_0 \
> -DBoost_LIBRARY_DIRS:STRING=/home/snorouzi/programs/boost_1_82_0/stage/lib
> \
> -DBoost_INCLUDE_DIRS:PATH=/home/snorouzi/programs/boost_1_82_0 \
> -DPYTHON_EXECUTABLE:FILEPATH=/usr/local/bin/python3.10
>
>
>
>
>
> csg_get_property: returning emtpy value for 'cg.non-bonded.inverse.imc.reg'
> Running subscript 'check_csg_xml.py
> /data/snorouzi/data/ibi_PLA/VOTCA_newversion/settings.xml
> /home/snorouzi/programs/VOTCA/installdir/share/votca/xml/csg_defaults.xml'
> (from tags check csg_xml) dir
> /home/snorouzi/programs/VOTCA/installdir/share/votca/scripts/inverse
>   File
> "/home/snorouzi/programs/VOTCA/installdir/share/votca/scripts/inverse/check_csg_xml.py",
> line 76
> child_path = f"{path}/{child.tag}"
>
This is a bit strange as check_csg_xml.py explicitly calls for python3:

https://github.com/votca/votca/blob/master/csg/share/scripts/inverse/check_csg_xml.py#L1
Anyhow as a workaround just make there is a python3 in your path that
points to your /usr/local/bin/python3.10.
E.g.
echo $PATH # pick a path
cd /home/christoph/.local/bin # e.g. this one
ln -s /usr/local/bin/python3.10 python3 # link it.

Christoph

 ^
> SyntaxError: invalid syntax
>
> Callstack:
> /home/snorouzi/programs/VOTCA/installdir/share/votca/scripts/inverse/inverse.sh
> - linenumber 111
> do_external - linenumber 183 in
> /home/snorouzi/programs/VOTCA/installdir/share/votca/scripts/inverse/functions_common.sh
>
>
> On Wed, Aug 9, 2023 at 8:35 PM Christoph Junghans 
> wrote:
>
>>
>>
>> On Wed, Aug 9, 2023 at 10:31 AM Saeed Norouzi 
>> wrote:
>>
>>> Dear  Christoph,
>>>
>>> I am trying to install the new version, but there is an error with cmake
>>> --build builddir.
>>>
>>> [ 10%] Building CXX object
>>> tools/src/libtools/CMakeFiles/votca_tools.dir/optionshandler.cc.o
>>> [ 11%] Building CXX object
>>> tools/src/libtools/CMakeFiles/votca_tools.dir/property.cc.o
>>> [ 11%] Building CXX object
>>> tools/src/libtools/CMakeFiles/votca_tools.dir/propertyiomanipulator.cc.o
>>> [ 12%] Building CXX object
>>> tools/src/libtools/CMakeFiles/votca_tools.dir/rangeparser.cc.o
>>> [ 12%] Building CXX object
>>> tools/src/libtools/CMakeFiles/votca_tools.dir/reducededge.cc.o
>>> [ 12%] Building CXX object
>>> tools/src/libtools/CMakeFiles/votca_tools.dir/reducedgraph.cc.o
>>> [ 13%] Building CXX object
>>> tools/src/libtools/CMakeFiles/votca_tools.dir/spline.cc.o
>>> [ 13%] Building CXX object
>>> tools/src/libtools/CMakeFiles/votca_tools.dir/table.cc.o
>>> [ 13%] Building CXX object
>>> tools/src/libtools/CMakeFiles/votca_tools.dir/thread.cc.o
>>> [ 14%] Building CXX object
>>> tools/src/libtools/CMakeFiles/votca_tools.dir/tokenizer.cc.o
>>> [ 14%] Building CXX object
>>> tools/src/libtools/CMakeFiles/votca_tools.dir/version.cc.o
>>> [ 15%] Linking CXX shared library libvotca_tools.so
>>> [ 15%] Built target votca_tools
>>> [ 16%] Building CXX object
>>> tools/src/tools/CMakeFiles/votca_property.dir/votca_property.cc.o
>>> [ 16%] Linking CXX executable votca_property
>>> [ 16%] Built target votca_property
>>> [ 16%] Building votca_property manpage
>>>   File
>>> "/home/snorouzi/programs/VOTCA/votca/tools/scripts/votca_help2doc", line 34
>>> """
>>>   ^
>>> SyntaxError: invalid syntax
>>>
>> Hmm, something seems to be wrong with your python install...
>> Can you look at the output from the previous cmake command, which python
>> was found?
>> You can also try to disable the manpage build with  -DBUILD_MANPAGES=OFF.
>>
>> Christoph
>>
>>
>>
>&g

Re: [votca] "Partial potential fitting" with force matching

[Christoph Junghans]

On Wed, Aug 9, 2023 at 10:32 AM Cecília Álvares
 wrote:
>
> Hmm.. now that I am ruminating about it, I dont think that it would work if I 
> did things in the way that I said it.. because VOTCA will still include the 
> superatoms type B in the system of equation: i.e., it will create equations 
> Fi = blabla for the superatoms type B within the overdetermined system of 
> equations... and, in these equations for superatoms type B, I would have only 
> the force-field of A-B trying to live up to the total force Fi experienced by 
> these superatoms (which is not true in practice since the B-B interactions 
> still exist: I was just trying to not concern them in the fit and get the 
> optimal A-B and A-A).
> Right? :///
> I guess I would not only have to not declare hte B-B interaction in the 
> fm.xml file but also I would need a way to delete Fi = blabla equations 
> formed by superatoms i whose type is B, I guess.
>
> I will check the method you mentioned carefully and I come back if the issue 
> still exists..!
Make sense, you can do a gromacs rerun with a topology where you
exclude all B-B forces and then run force matching on the new
trajectory like we did in that paper.

Christoph

>
> Thanks,
> Cecilia
>
> Em quarta-feira, 9 de agosto de 2023 às 00:35:22 UTC+2, Christoph Junghans 
> escreveu:
>>
>> On Tue, Aug 8, 2023 at 3:26 PM Cecília Álvares
>>  wrote:
>> >
>> > Hello!
>> >
>> > Quick question: suppose I have a system in its all-atom representation and 
>> > I want to use it as reference to derive CG force-fields via 
>> > force-matching. For that I have a trajectory file containing the position 
>> > of all atoms and the force experienced by each of them.
>> >
>> > The all-atom system has several atom types while its corresponding 
>> > coarse-grained counterpart shall have only two superatom types (let's call 
>> > them A and B) which are not bonded.
>> >
>> > Let's suppose that for some reason I am only interested in the pairwise CG 
>> > interactions A-A and A-B. Is it okay in the eyes of VOTCA if I declare in 
>> > the fmatch.xml file only these two interactions? Would it give me correct 
>> > potentials? What I mean is: will the algorithm, in the way it is 
>> > implemented, give me the force-fields A-A and A-B that minimize the error 
>> > of the overdetermined system of equations without considering at all the 
>> > interaction B-B? (i.e., superatoms type B would exist in this context 
>> > merely because I need to parametrize A-B and thus they will participate in 
>> > that manner)
>> > Or will the results VOTCA outputs be wrong for some reason?
>> It should work! Another way would be to subtract the B-B force from
>> the trajectory before doing forcematching. Similar to what we did
>> here: http://dx.doi.org/10.1002/mats.201100011
>>
>> Christoph
>> >
>> > Thanks in advance,
>> > Cecilia
>> >
>> > --
>> > Join us on Slack: https://join.slack.com/t/votca/signup
>> > ---
>> > You received this message because you are subscribed to the Google Groups 
>> > "votca" group.
>> > To unsubscribe from this group and stop receiving emails from it, send an 
>> > email to votca+un...@googlegroups.com.
>> > To view this discussion on the web visit 
>> > https://groups.google.com/d/msgid/votca/7e119f2b-88b2-4686-815a-f0c6c1d6a565n%40googlegroups.com.
>>
>>
>>
>> --
>> Christoph Junghans
>> Web: http://www.compphys.de
>
> --
> Join us on Slack: https://join.slack.com/t/votca/signup
> ---
> You received this message because you are subscribed to the Google Groups 
> "votca" group.
> To unsubscribe from this group and stop receiving emails from it, send an 
> email to votca+unsubscr...@googlegroups.com.
> To view this discussion on the web visit 
> https://groups.google.com/d/msgid/votca/a08e6198-2263-4957-ac5f-3332e5f2f8ean%40googlegroups.com.



-- 
Christoph Junghans
Web: http://www.compphys.de

-- 
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Re: [votca] Problem with extrapolation for bonds

[Christoph Junghans]

On Wed, Aug 9, 2023 at 10:31 AM Saeed Norouzi  wrote:

> Dear  Christoph,
>
> I am trying to install the new version, but there is an error with cmake
> --build builddir.
>
> [ 10%] Building CXX object
> tools/src/libtools/CMakeFiles/votca_tools.dir/optionshandler.cc.o
> [ 11%] Building CXX object
> tools/src/libtools/CMakeFiles/votca_tools.dir/property.cc.o
> [ 11%] Building CXX object
> tools/src/libtools/CMakeFiles/votca_tools.dir/propertyiomanipulator.cc.o
> [ 12%] Building CXX object
> tools/src/libtools/CMakeFiles/votca_tools.dir/rangeparser.cc.o
> [ 12%] Building CXX object
> tools/src/libtools/CMakeFiles/votca_tools.dir/reducededge.cc.o
> [ 12%] Building CXX object
> tools/src/libtools/CMakeFiles/votca_tools.dir/reducedgraph.cc.o
> [ 13%] Building CXX object
> tools/src/libtools/CMakeFiles/votca_tools.dir/spline.cc.o
> [ 13%] Building CXX object
> tools/src/libtools/CMakeFiles/votca_tools.dir/table.cc.o
> [ 13%] Building CXX object
> tools/src/libtools/CMakeFiles/votca_tools.dir/thread.cc.o
> [ 14%] Building CXX object
> tools/src/libtools/CMakeFiles/votca_tools.dir/tokenizer.cc.o
> [ 14%] Building CXX object
> tools/src/libtools/CMakeFiles/votca_tools.dir/version.cc.o
> [ 15%] Linking CXX shared library libvotca_tools.so
> [ 15%] Built target votca_tools
> [ 16%] Building CXX object
> tools/src/tools/CMakeFiles/votca_property.dir/votca_property.cc.o
> [ 16%] Linking CXX executable votca_property
> [ 16%] Built target votca_property
> [ 16%] Building votca_property manpage
>   File "/home/snorouzi/programs/VOTCA/votca/tools/scripts/votca_help2doc",
> line 34
> """
>   ^
> SyntaxError: invalid syntax
>
Hmm, something seems to be wrong with your python install...
Can you look at the output from the previous cmake command, which python
was found?
You can also try to disable the manpage build with  -DBUILD_MANPAGES=OFF.

Christoph



> tools/src/tools/CMakeFiles/votca_property_manpage.dir/build.make:73:
> recipe for target 'tools/src/tools/votca_property.man' failed
> gmake[2]: *** [tools/src/tools/votca_property.man] Error 1
> CMakeFiles/Makefile2:1588: recipe for target
> 'tools/src/tools/CMakeFiles/votca_property_manpage.dir/all' failed
> gmake[1]: *** [tools/src/tools/CMakeFiles/votca_property_manpage.dir/all]
> Error 2
> Makefile:145: recipe for target 'all' failed
> gmake: *** [all] Error 2
> [snorouzi@master VOTCA]
>
> On Wed, Aug 9, 2023 at 3:02 PM Christoph Junghans 
> wrote:
>
>>
>>
>> On Wed, Aug 9, 2023, 02:56 Saeed Norouzi  wrote:
>>
>>> Dear Christoph,
>>>
>>> Thank you for your reply. making the range smaller did not help me.
>>> Still the same problem, but I tried to use the higher step size and it
>>> helps with the extrapolation a little bit (the wrong extrapolation happens
>>> less frequently, also using different extrapolation functions improves it).
>>> I have another problem with the dihedrals. My target distribution for
>>> dihedrals is not periodic (means the both ends are not same -pi and pi). I
>>> have the setting for the dihedrals below. Do you know how I can fix
>>> this problem? By the way, I a, using  votca/gcc/single/dev-25Jan19.
>>>
>> If that stands for 25 Jan 2019, I think you will need to update first. We
>> had a couple of dihedral improvements in the meanwhile and it is hard to
>> work around bugs in old versions.
>>
>> Christoph
>>
>>
>>
>>> 
>>> dihedral.1
>>> -3.1415
>>> 3.1415
>>> 0.02
>>> 
>>> 
>>> dihedral.2
>>> -3.1415
>>> 3.1415
>>> 0.01
>>> 
>>> 
>>> dihedral.3
>>> -3.1415
>>> 3.1415
>>> 0.02
>>> 
>>> [image: Screenshot from 2023-08-09 10-56-13.png]
>>>
>>> [image: Screenshot from 2023-08-09 10-55-39.png]
>>>
>>> On Fri, Aug 4, 2023 at 5:31 PM Christoph Junghans 
>>> wrote:
>>>
>>>>
>>>>
>>>> On Fri, Aug 4, 2023 at 02:18 Saeed Norouzi 
>>>> wrote:
>>>>
>>>>> Dear Christoph and Votca users,
>>>>>
>>>>>
>>>>> I have an annoying problem with the bonded interactions in my coarse
>>>>> grained model. mainly its because of the bond potential which lets the 
>>>>> bond
>>>>> length > table cut off in my lammps simulations.  as far as I know the
>>>>> potential that I get from th

Re: [votca] Problem with extrapolation for bonds

[Christoph Junghans]

On Wed, Aug 9, 2023, 02:56 Saeed Norouzi  wrote:

> Dear Christoph,
>
> Thank you for your reply. making the range smaller did not help me. Still
> the same problem, but I tried to use the higher step size and it helps with
> the extrapolation a little bit (the wrong extrapolation happens less
> frequently, also using different extrapolation functions improves it). I
> have another problem with the dihedrals. My target distribution for
> dihedrals is not periodic (means the both ends are not same -pi and pi). I
> have the setting for the dihedrals below. Do you know how I can fix
> this problem? By the way, I a, using  votca/gcc/single/dev-25Jan19.
>
If that stands for 25 Jan 2019, I think you will need to update first. We
had a couple of dihedral improvements in the meanwhile and it is hard to
work around bugs in old versions.

Christoph



> 
> dihedral.1
> -3.1415
> 3.1415
> 0.02
> 
> 
> dihedral.2
> -3.1415
> 3.1415
> 0.01
> 
> 
> dihedral.3
> -3.1415
> 3.1415
> 0.02
> 
> [image: Screenshot from 2023-08-09 10-56-13.png]
>
> [image: Screenshot from 2023-08-09 10-55-39.png]
>
> On Fri, Aug 4, 2023 at 5:31 PM Christoph Junghans 
> wrote:
>
>>
>>
>> On Fri, Aug 4, 2023 at 02:18 Saeed Norouzi  wrote:
>>
>>> Dear Christoph and Votca users,
>>>
>>>
>>> I have an annoying problem with the bonded interactions in my coarse
>>> grained model. mainly its because of the bond potential which lets the bond
>>> length > table cut off in my lammps simulations.  as far as I know the
>>> potential that I get from the votca seems smooth enough (to not have high
>>> values for forces in lammps simulations), but I get a weird extrapolation
>>> for both ends. I have attached the picture of bond energy, the bond target
>>> distribution and also the .xml for the  bond. I would really appreciate
>>> your help with this.
>>>
>> i saw that issue before, try to make range smaller by increasing min and
>> decreasing the max, that hopefully helps to get the slop and hence the
>> extrapolation right.
>>
>> Christoph
>>
>>
>>
>>>  
>>>
>>> 
>>>
>>>   
>>> 
>>> bond.1
>>> 3.39
>>> 3.84
>>> 0.001
>>> 
>>>   
>>>   bond.1.dist.tgt
>>>   1
>>>
>>> table_b1.xvg
>>> 0.0001
>>> 5
>>> 0.0001
>>>
>>> 
>>>   [image: Figure_1.png]
>>>
>>> --
>>> Join us on Slack: https://join.slack.com/t/votca/signup
>>> ---
>>> You received this message because you are subscribed to the Google
>>> Groups "votca" group.
>>> To unsubscribe from this group and stop receiving emails from it, send
>>> an email to votca+unsubscr...@googlegroups.com.
>>> To view this discussion on the web visit
>>> https://groups.google.com/d/msgid/votca/CAJZjMJYrs%3DyvnHDgB3RVJkxDPqM3mDOFP9-h4NrfZ9j%3DyoZmqA%40mail.gmail.com
>>> <https://groups.google.com/d/msgid/votca/CAJZjMJYrs%3DyvnHDgB3RVJkxDPqM3mDOFP9-h4NrfZ9j%3DyoZmqA%40mail.gmail.com?utm_medium=email_source=footer>
>>> .
>>>
>> --
>> Christoph Junghans
>> Web: http://www.compphys.de
>>
>> --
>> Join us on Slack: https://join.slack.com/t/votca/signup
>> ---
>> You received this message because you are subscribed to the Google Groups
>> "votca" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to votca+unsubscr...@googlegroups.com.
>> To view this discussion on the web visit
>> https://groups.google.com/d/msgid/votca/CAHG27e4jVSaA%3Dtq1r7%2BisdtnzUEtKuSZreLU7dVbYNw93%2BGWRA%40mail.gmail.com
>> <https://groups.google.com/d/msgid/votca/CAHG27e4jVSaA%3Dtq1r7%2BisdtnzUEtKuSZreLU7dVbYNw93%2BGWRA%40mail.gmail.com?utm_medium=email_source=footer>
>> .
>>
> --
> Join us on Slack: https://join.slack.com/t/votca/signup
> ---
> You received this message because you are subscribed to the Google Groups
> "votca" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to votca+unsubscr...@googlegroups.com.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/votca/CAJZjMJb0Be_5LjY81tTFtuJabO2Z%3Dgtc_7d21Bq7Cn06G-7Bsw%40mail.gmail.com
> <https://groups.google.com/d/msgid/votca/CAJZjMJb0Be_5LjY81tTFtuJabO2Z%3Dgtc_7d21Bq7Cn06G-7Bsw%40mail.gmail.com?utm_medium=email_source=footer>
> .
>

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Re: [votca] "Partial potential fitting" with force matching

[Christoph Junghans]

On Tue, Aug 8, 2023 at 3:26 PM Cecília Álvares
 wrote:
>
> Hello!
>
> Quick question: suppose I have a system in its all-atom representation and I 
> want to use it as reference to derive CG force-fields via force-matching. For 
> that I have a trajectory file containing the position of all atoms and the 
> force experienced by each of them.
>
> The all-atom system has several atom types while its corresponding 
> coarse-grained counterpart shall have only two superatom types (let's call 
> them A and B) which are not bonded.
>
> Let's suppose that for some reason I am only interested in the pairwise CG 
> interactions A-A and A-B. Is it okay in the eyes of VOTCA if I declare in the 
> fmatch.xml file only these two interactions? Would it give me correct 
> potentials? What I mean is: will the algorithm, in the way it is implemented, 
> give me the force-fields A-A and A-B that minimize the error of the 
> overdetermined system of equations without considering at all the interaction 
> B-B? (i.e., superatoms type B would exist in this context merely because I 
> need to parametrize A-B and thus they will participate in that manner)
> Or will the results VOTCA outputs be wrong for some reason?
It should work! Another way would be to subtract the B-B force from
the trajectory before doing forcematching. Similar to what we did
here: http://dx.doi.org/10.1002/mats.201100011

Christoph
>
> Thanks in advance,
> Cecilia
>
> --
> Join us on Slack: https://join.slack.com/t/votca/signup
> ---
> You received this message because you are subscribed to the Google Groups 
> "votca" group.
> To unsubscribe from this group and stop receiving emails from it, send an 
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Re: [votca] Problem with extrapolation for bonds

[Christoph Junghans]

On Fri, Aug 4, 2023 at 02:18 Saeed Norouzi  wrote:

> Dear Christoph and Votca users,
>
>
> I have an annoying problem with the bonded interactions in my coarse
> grained model. mainly its because of the bond potential which lets the bond
> length > table cut off in my lammps simulations.  as far as I know the
> potential that I get from the votca seems smooth enough (to not have high
> values for forces in lammps simulations), but I get a weird extrapolation
> for both ends. I have attached the picture of bond energy, the bond target
> distribution and also the .xml for the  bond. I would really appreciate
> your help with this.
>
i saw that issue before, try to make range smaller by increasing min and
decreasing the max, that hopefully helps to get the slop and hence the
extrapolation right.

Christoph



>  
>
> 
>
>   
> 
> bond.1
> 3.39
> 3.84
> 0.001
> 
>   
>   bond.1.dist.tgt
>   1
>
> table_b1.xvg
> 0.0001
> 5
> 0.0001
>
> 
>   [image: Figure_1.png]
>
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Re: [votca] Re: VOTCA interpretation units dump file

[Christoph Junghans]

On Fri, Jul 28, 2023, 01:40 Cecília Álvares 
wrote:

> Hey Christoph,
>
> But in fact, even if my forces in the dump file are saved in
> kcal/(mol.ang), the unit for the force output in the .force files is in
> kJ/(mol.nm)? Is that it?
>
Correct!



>
> Em quinta-feira, 27 de julho de 2023 às 19:48:09 UTC+2, Christoph Junghans
> escreveu:
>
>> On Thu, Jul 27, 2023 at 11:41 AM Cecília Álvares
>>  wrote:
>> >
>> > PS: I am talking about the units in the .force output files (i.e., the
>> ones we obtain by simply doing the csg_fmatch command, with no further
>> commands) and considering that there is no unit conversion information in
>> my fmatch.xml file.
>>
>> Yes, we use the same unit system as gromacs:
>>
>> https://manual.gromacs.org/documentation/2019/reference-manual/definitions.htm,
>>
>> so kJ mol−1 nm−1 for the forces.
>> But we also assume the positions are in Ang, so there might be a
>> factor 10 somewhere.
>>
>> https://github.com/votca/votca/blob/master/csg/src/libcsg/modules/io/lammpsdumpreader.cc#L217
>> and we assume the forces in the dump file are in kcal/ang.
>>
>> https://github.com/votca/votca/blob/master/csg/src/libcsg/modules/io/lammpsdumpreader.cc#L243
>>
>> if that isn't the case for your dump you will need to apply some
>> scaling factor to the .force file afterwards.
>> >
>> > Em quinta-feira, 27 de julho de 2023 às 19:39:19 UTC+2, Cecília Álvares
>> escreveu:
>> >>
>> >> Hello,
>> >>
>> >> I am using a trajectory in the .dump format to derive CG potentials
>> using FM. My dump file contains 8 columns (atom ID, atom type, the three
>> coordinates, the force components in each of the three directions).
>> >>
>> >> When doing some tests, I came to realize that if I feed VOTCA with a
>> .dump trajectory file containing unscaled coordinates in angstroms, it
>> gives me the same result as if I had fed it the scaled coordinates. So I
>> suppose in its internal script, VOTCA has as the standard unit of the
>> unscaled coordinates in a .dump file to be angs (right?). I was wondering
>> if VOTCA has a special default unit for the forces that are in the .dump
>> file. What is VOTCA going to interpret the unit of the force components as?
>> Something like kJ/(mol.angs) maybe?
>> >
>> > --
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>>
>>
>>
>>
>> --
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>> Web: http://www.compphys.de
>>
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Re: [votca] Re: VOTCA interpretation units dump file

[Christoph Junghans]

On Thu, Jul 27, 2023 at 11:41 AM Cecília Álvares
 wrote:
>
> PS: I am talking about the units in the .force output files (i.e., the ones 
> we obtain by simply doing the csg_fmatch command, with no further commands) 
> and considering that there is no unit conversion information in my fmatch.xml 
> file.

Yes, we use the same unit system as gromacs:
https://manual.gromacs.org/documentation/2019/reference-manual/definitions.htm,
so kJ mol−1 nm−1 for the forces.
But we also assume the positions are in Ang, so there might be a
factor 10 somewhere.
https://github.com/votca/votca/blob/master/csg/src/libcsg/modules/io/lammpsdumpreader.cc#L217
and we assume the forces in the dump file are in kcal/ang.
https://github.com/votca/votca/blob/master/csg/src/libcsg/modules/io/lammpsdumpreader.cc#L243

if that isn't the case for your dump you will need to apply some
scaling factor to the .force file afterwards.
>
> Em quinta-feira, 27 de julho de 2023 às 19:39:19 UTC+2, Cecília Álvares 
> escreveu:
>>
>> Hello,
>>
>> I am using a trajectory in the .dump format to derive CG potentials using 
>> FM. My dump file contains 8 columns (atom ID, atom type, the three 
>> coordinates, the force components in each of the three directions).
>>
>> When doing some tests, I came to realize that if I feed VOTCA with a .dump 
>> trajectory file containing unscaled coordinates in angstroms, it gives me 
>> the same result as if I had fed it the scaled coordinates. So I suppose in 
>> its internal script, VOTCA has as the standard unit of the unscaled 
>> coordinates in a .dump file to be angs (right?). I was wondering if VOTCA 
>> has a special default unit for the forces that are in the .dump file. What 
>> is VOTCA going to interpret the unit of the force components as? Something 
>> like kJ/(mol.angs) maybe?
>
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Re: [votca] RDF peak for non-bonded interaction not converging

[Christoph Junghans]

On Thu, Jul 6, 2023 at 10:51 AM Sanjeet Singh  wrote:
>
> Hello Christoph,
>
> If I update only one interaction for a while, then is it okay to use scale 
> factor of 1.0 for the interaction?
Yes.
>
> And also the pressure correction settings should be kept same as in the 
> multiple interactions?
I would try without pressure correction and try to get the RDF right first.

Christoph
>
> Thank you,
> Sanjeet
>
> On Thursday, July 6, 2023 at 11:18:22 AM UTC-4 Sanjeet Singh wrote:
>>
>> Hello Christoph,
>>
>> Thank you for your reply.
>>
>> Can you please tell me that Can I improve the convergence by increasing the 
>> scale factor?
>>
>> Thank you,
>> Sanjeet
>>
>> On Wednesday, July 5, 2023 at 12:43:36 PM UTC-4 Christoph Junghans wrote:
>>>
>>> On Wed, Jul 5, 2023 at 5:35 AM Sanjeet Singh  wrote:
>>> >
>>> > Hello all,
>>> >
>>> > I am trying to perform IBI on non-bonded interaction for a polymer. But 
>>> > even after 200 iterations IBI is not able to reproduce the peak of the 
>>> > RDF. After 180 iterations nothing is changing much in the system.
>>> >
>>> > Earlier, when I use to do IBI for small systems it use to converge 
>>> > completely.
>>> >
>>> > Is it related to scaling factor??? If yes, then how much should I 
>>> > increase it??
>>> >
>>> > I have 6 non-bonded interactions in my system. I am using 0.25 as scale 
>>> > factor for the interaction I am talking about here, and for the remaining 
>>> > I am using 0.16.
>>> >
>>> > The similar problem is there for other non-bonded pairs also, but this 
>>> > pair is the major non-bonded pair of my system.
>>> >
>>> > I am attaching the plot for reference.
>>> >
>>> > I would be grateful for any suggestions.
>>> Mavin is the expert on this matter, but I would try to only update the
>>> one interaction for a while and go back to the multiple interactiones
>>> update scheme.
>>>
>>> Christoph
>>>
>>> >
>>> > Thank you.
>>> > Sanjeet
>>> >
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>>>
>>>
>>>
>>> --
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>>> Web: http://www.compphys.de
>
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Re: [votca] RDF peak for non-bonded interaction not converging

[Christoph Junghans]

On Wed, Jul 5, 2023 at 5:35 AM Sanjeet Singh  wrote:
>
> Hello all,
>
> I am trying to perform IBI on non-bonded interaction for a polymer. But even 
> after 200 iterations IBI is not able to reproduce the peak of the RDF. After 
> 180 iterations nothing is changing much in the system.
>
> Earlier, when I use to do IBI for small systems it use to converge completely.
>
> Is it related to scaling factor??? If yes, then how much should I increase 
> it??
>
> I have 6 non-bonded interactions in my system. I am using 0.25 as scale 
> factor for the interaction I am talking about here, and for the remaining I 
> am using 0.16.
>
> The similar problem is there for other non-bonded pairs also, but this pair 
> is the major non-bonded pair of my system.
>
> I am attaching the plot for reference.
>
> I would be grateful for any suggestions.
Mavin is the expert on this matter, but I would try to only update the
one interaction for a while and go back to the multiple interactiones
update scheme.

Christoph

>
> Thank you.
> Sanjeet
>
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Re: [votca] csg_dump creates different results for LAMMPS and GROMACS

[Christoph Junghans]

On Wed, Jul 5, 2023 at 6:47 AM Philipp Rosenauer  wrote:
>
> Hello everyone,
>
> I want to use VOTCA with LAMMPS to coarse-grain a polyimide. I started to 
> work with VOTCA by following the tutorials and found that most tutorials are 
> only for Gromacs so I also took a look at Gromacs and did the hexane 
> tutorial. To learn everything for the big polymer I wanted to rebuild the 
> Tutorial for LAMMPS but during the csg_stat I discovered some problems. The 
> RDFs were quite different.
>
> So I went back and just did a simulation in LAMMPS and GROMACS with all 
> forces set to zero. I also checked the coordinates for both LAMMPS (in an 
> .xtc format) and the GROMACS .trj file and they were identical for all 1000 
> timesteps.
>
> I also have the same --cg file: hexane.xml (only changed the names of the 
> molecules accordingly to the output of csg_dump)
>
> I then proceeded with the following commands:
> For LAMMPS:
>
> csg_stat --top topo.xml --trj gromacs.xtc --cg hexane.xml --nt 24 --options 
> settings.xml --begin 0
>
> For Gromacs:
>
> csg_stat --top topol.tpr --trj traj.trr --cg hexane.xml --nt 24 --options 
> settings.xml --begin 0
>
> So the hexane.xml files as well as the settings.xml files are identical.I 
> assumed that the results should be the same but still the rdfs are different 
> (see picture of nonbonded A-A below)
>
> I attach the topo.xml file for the LAMMPS side and the settings.xml file as 
> well and would appreciate every help I could get to understand where the 
> mistake happens.

My guess is that the tpr file has some exclusions in it and the xml
topology doesn't.
You can check that by using the topol.xml with the traj.trr or by
running csg_dump --top  --excl and compare the output.
You can add exclusion to a topology by adding bonds, angle etc to the
mapping file.
>
>
>
>
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Re: [votca] Regarding-Getting-itp-files:

[Christoph Junghans]

On Fri, Jun 30, 2023, 02:36 Kankana Bhattacharjee <
kankanabhattacharje...@gmail.com> wrote:

>
> Sir, During mapping using (csg_map) votca one tpr file is needed. But, if
> I want to convert an arbitrary AA structure into CG structure then which
> tpr file has to be provided? I mean energy minimised ya final npt
> production run tor file ?
>
It doesn't really matter, VOTCA just reads the topology information from
the tpr, not positions etc.


> On Wed, Jun 28, 2023, 18:47 Christoph Junghans  wrote:
>
>>
>>
>> On Tue, Jun 27, 2023 at 9:57 PM Kankana Bhattacharjee <
>> kankanabhattacharje...@gmail.com> wrote:
>>
>>> Sir, what would be the typical force constant value in case of angle for
>>> CG propane if I Don't use tabulated functional form?
>>>
>> I am not sure out of my head, it has been too long.
>> You could make an estimate from Figure 4d of
>> http://dx.doi.org/10.1021/ct900369w.
>>
>>
>>> On Tue, Jun 27, 2023, 18:28 Christoph Junghans 
>>> wrote:
>>>
>>>>
>>>>
>>>> On Tue, Jun 27, 2023, 05:18 Kankana Bhattacharjee <
>>>> kankanabhattacharje...@gmail.com> wrote:
>>>>
>>>>> Ok. Thank you sir.
>>>>>
>>>>> Sir, I have got the bond length, angle distribution datas from the
>>>>> atomistic simulation using gmx distance and angle options respectively.
>>>>> But, how can I invert the bonded potentials i.e, bonded potential plots ?
>>>>> Initially, using csg_boltzmann I used the command line:
>>>>>
>>>>> csg_boltzmann --top topol.tpr --trj traj.trr --cg propane.xml <
>>>>> boltzmann_cmds
>>>>>  From there, I obtained the inverted curve. I would like to fit the
>>>>> all atom bonded datas to get the force constant. So, for that I need to
>>>>> convert the output file (aa-dist.xvg, aa-angle-dist.xvg). How to do that
>>>>> job ? Can it be done using:
>>>>> csg_boltzmann --top topol.tpr --trj traj.trr (the trajectory which
>>>>> used to get the distribution) --no-map <  boltzmann_cmds
>>>>>
>>>> Sorry, but VOTCA doesn't have a tool to fit force constants! I would
>>>> recommend using gnuplot or numpy for that.
>>>>
>>>>
>>>>>
>>>>>> On Tue, Jun 27, 2023 at 4:34 PM Christoph Junghans <
>>>>> jungh...@votca.org> wrote:
>>>>>
>>>>>>
>>>>>>
>>>>>> On Tue, Jun 27, 2023, 04:13 Kankana Bhattacharjee <
>>>>>> kankanabhattacharje...@gmail.com> wrote:
>>>>>>
>>>>>>>
>>>>>>> Sir, I want to convert an atomistic structure into CG by providing
>>>>>>> the mapping file but for specific molecule I want to ignore the mapping.
>>>>>>> How to do that using csg_map tool ? As csg_map is having only --no-map
>>>>>>> option ? How can I ignore the mapping for specific molecule during the
>>>>>>> conversion process using csg_map tool ?
>>>>>>>
>>>>>> There is a --map-ignore option.
>>>>>> See https://www.votca.org/csg/reference.html#csg-map
>>>>>>
>>>>>>
>>>>>>> Your suggestions would be much appreciated.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> [image: Mailtrack]
>>>>>>> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>>>>>>>  Sender
>>>>>>> notified by
>>>>>>> Mailtrack
>>>>>>> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>>>>>>>  06/27/23,
>>>>>>> 03:39:45 PM
>>>>>>>
>>>>>>> On Wed, Jun 21, 2023 at 8:48 PM Christoph Junghans <
>>>>>>> jungh...@votca.org> wrote:
>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On Wed, Jun 21, 2023 at 7:21 AM Kankana Bhattacharjee <
>>>>>>>> kankanabhattacharje...@gmail.com> wrote:
>>>>>>>>
>>>>>>>>> Sir, I have attached the ppt where bond length distribution of AA
>>>>>>>>> and CG run is attached. I used gmx distance to plot the 

[votca] Fwd: 2023 LAMMPS Workshop & Symposium

[Christoph Junghans]

If you are doing anything with VOTCA and LAMMPS, the venue below might
be a good chance to present.

Christoph

-- Forwarded message -
From: "Moore, Stan"
Date: Monday, June 26, 2023 at 16:32
Subject: [EXTERNAL] 2023 LAMMPS Workshop & Symposium



Hi Everyone,



As an attendee of the previous virtual LAMMPS
workshop in 2021, we wanted to make you aware that we will be holding
another LAMMPS Workshop & Symposium this year on August 8-11, 2023. We
have decided to make it a virtual event again using Zoom.



This is a great venue to present your modeling results to others and
get useful feedback or trigger collaborations. This year there will be
a mix of invited, contributed, and lightning talks (in place of
posters), as well as a beginners tutorial and developers discussion,
and possibly one-hour breakout sessions devoted to specific topics.



We still have room for more contributed talks. The registration
deadline to present a talk (regular or lightning) is this Friday, June
30th. There is no fee to attend the workshop. You can register here:



https://docs.google.com/forms/d/e/1FAIpQLSf3LUjky-KRdgfCCrK1P-bjQfMoU--KN00NEFXlSBFa4Ykiww/viewform



Please feel free to reach out if you have any questions.



Regards,





Stan Moore

LAMMPS developer





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Re: [votca] Regarding-Getting-itp-files:

[Christoph Junghans]

On Tue, Jun 27, 2023, 04:13 Kankana Bhattacharjee <
kankanabhattacharje...@gmail.com> wrote:

>
> Sir, I want to convert an atomistic structure into CG by providing the
> mapping file but for specific molecule I want to ignore the mapping. How to
> do that using csg_map tool ? As csg_map is having only --no-map option ?
> How can I ignore the mapping for specific molecule during the conversion
> process using csg_map tool ?
>
There is a --map-ignore option.
See https://www.votca.org/csg/reference.html#csg-map


> Your suggestions would be much appreciated.
>
>
>
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>
> On Wed, Jun 21, 2023 at 8:48 PM Christoph Junghans 
> wrote:
>
>>
>>
>> On Wed, Jun 21, 2023 at 7:21 AM Kankana Bhattacharjee <
>> kankanabhattacharje...@gmail.com> wrote:
>>
>>> Sir, I have attached the ppt where bond length distribution of AA and CG
>>> run is attached. I used gmx distance to plot the distance distribution.
>>>
>> Looks like your system gets stuck  around 0.075nm, what is the minimum of
>> your IB potential for the bond?
>>
>> Christoph
>>
>>>
>>> On Wed, Jun 21, 2023 at 6:36 PM Christoph Junghans 
>>> wrote:
>>>
>>>>
>>>>
>>>> On Tue, Jun 20, 2023 at 9:57 PM Kankana Bhattacharjee <
>>>> kankanabhattacharje...@gmail.com> wrote:
>>>>
>>>>> Sir, I am not getting the same atomistic bonded distribution in case
>>>>> of CG run of propane. I used the atomistic grompp.mdp file for the CG
>>>>> propane vacuum simulation. Kindly suggest me what should I do to fix this 
>>>>> ?
>>>>>
>>>> I don't think the parameters in the mdp file play a bit role as long as
>>>> as you sample the same ensemble (NVT) and density (molecules per box). How
>>>> different are the distributions? For non-iterative Boltzmann inversion, it
>>>> will never match a 100%, hence most folks do iterative boltzmann inversion.
>>>>
>>>> Christoph
>>>>
>>>>>
>>>>> On Tue, Jun 20, 2023 at 6:48 PM Kankana Bhattacharjee <
>>>>> kankanabhattacharje...@gmail.com> wrote:
>>>>>
>>>>>> Yes sir.
>>>>>>
>>>>>> On Tue, Jun 20, 2023 at 6:44 PM Christoph Junghans <
>>>>>> jungh...@votca.org> wrote:
>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Tue, Jun 20, 2023 at 4:07 AM Kankana Bhattacharjee <
>>>>>>> kankanabhattacharje...@gmail.com> wrote:
>>>>>>>
>>>>>>>> Sir, I ran the CGMD simulation using gromacs by providing the
>>>>>>>> grompp.mdp file of the atomistic run. I was not sure about that. In 
>>>>>>>> Votca
>>>>>>>> CG methods, grompp.mdp are different in both ibi and imc methods. And, 
>>>>>>>> the
>>>>>>>> bonded distributions of the CGMD run is not matching with the AA run at
>>>>>>>> all. I would like to know, which grompp.mdp file has to be provided 
>>>>>>>> for the
>>>>>>>> CGMD run using gromacs (I mean ibi ya imc one) ?
>>>>>>>>
>>>>>>> You mean this one:
>>>>>>>
>>>>>>> https://github.com/votca/votca/blob/master/csg-tutorials/propane/ibi/grompp.mdp
>>>>>>>
>>>>>>>
>>>>>>>> On Mon, Jun 19, 2023 at 11:46 PM Kankana Bhattacharjee <
>>>>>>>> kankanabhattacharje...@gmail.com> wrote:
>>>>>>>>
>>>>>>>>> Thanks Sir
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
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Re: [votca] Curious question FM unsampled regions

[Christoph Junghans]

On Wed, Jun 21, 2023, 06:26 Cecília Álvares 
wrote:

> Hey,
>
> I have a small question about the implementation of force-matching on
> VOTCA. It is advocated to always input a  and  value in the
> fmatch.xml file for which the degree of freedom (pair distance, for
> example) of the given interaction is continuously sampled. So for example,
> in my case, in which I am using a trajectory sampled in a xtalline state, I
> would not have that (the peaks in the RDF grow and go back to zero before
> meeting one another).
>
> In Sergei and Voth's official paper of force-matching, he says "*If a
> certain spline parameter is not explicitly present because the respective
> grid space is not sampled by a particular set of atomic configurations and,
> therefore, this parameter is not possible to determine, it can be safely
> assumed to be zero.*" ( - https://doi.org/10.1063/1.1739396). The core
> implementation of FM in VOTCA comes from Sergei and Voth's formalism in
> that paper, right? I was wondering why is it that this particular
> consideration he makes is not implemented in VOTCA, which instead gives an
> error if there are unsampled regios in the   range informed. Is
> there a reason why you guys thought it would not be suitable to use this
> assumption?
>
Not sure, but it was maybe just easier to implement it for one region. Not
many folks have asked for multiple regions over the decade since
force-matching was implemented, so I guess we weren't totally off.

Maybe you can have a look at the code:
https://github.com/votca/votca/blob/master/csg/src/tools/csg_fmatch.cc
and add that feature.

Christoph

>
> Best,
> Cecilia
>
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>

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[votca] Re: Types of Simulations using VOTCA

[Christoph Junghans]

On Mon, Jun 19, 2023 at 12:20 AM Gangotree Rai  wrote:
>
> Respected Sir,
> Can we do simulations of solvated polymer (polymer-surfactant) or ternary 
> type (polymer-surfactant-water) systems using VOTCA?
Yes, people did a lot of polymeric systems with VOTCA.
> And one more query: can we do the coarse-graining of charged macromolecules 
> (i.e., polyelectrolyte, surfactant, proteins) using VOTCA provided the charge 
> effects are also visible during CG simulations?
Yes, but VOTCA has no coarse-graining method implemented that knows
about charges, so you will have to treat coulomb outside of e.g. IBI.
I think this has been done with VOTCA before by N.R. Aluru's group out
of UI-UC, please check their publications.
In short if I remember correctly you can fit the tail of the PMF to
determine the charges and background epsilon and then use standard
coulomb and use IBI or IMC to improve the short range interactions.

Christoph
>
> --
> Thank you
> Warm Regards
> Gangotree Rai
> PhD | Chemical Engineering
> Macromolecular Modeling and Simulation Laboratory
> Indian Institute of Technology Madras (IITM)
> Chennai 600036, Tamil Nadu, India
> Ph: (O) +91-731-857-5569 (Call) | +91-876-574-7978 (w)
>
> Sender notified by
> Mailtrack 06/19/23, 11:45:58 AM



-- 
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Web: http://www.compphys.de

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[votca] Re: Votca compatibility in GROMACS

[Christoph Junghans]

On Sun, Jun 18, 2023 at 11:01 AM Gangotree Rai 
wrote:

> Thanks for your kind reply.
> Can I use the gromacs 2018.8 with tabulated function?
>
Technically yes, but in the latest version of VOTCA we removed support for
gromacs versions before 2019.
In VOTCA-2022 it should still work.


> On Sun, Jun 18, 2023, 21:50 Christoph Junghans  wrote:
>
>>
>>
>> On Sat, Jun 17, 2023 at 9:38 PM Gangotree Rai 
>> wrote:
>>
>>> Dear Sir,
>>> I am new to this VOTCA field and am trying to learn through the VOTCA
>>> manual and its tutorial. My basic doubt is whether I can use VOTCA in the
>>> GROMACS 2020 version or not since VOTCA simulations are carried out with
>>> the tabulated function (potential). If not, then please suggest which
>>> GROMACS version is compatible with VOTCA.
>>>
>> You need to use gromacs-2019! gromacs-2020 dropped the tabulated
>> potential feature and it hasn't been re-implemented since (see
>> https://gitlab.com/gromacs/gromacs/-/issues/1347 and
>> https://gromacs.bioexcel.eu/t/reimplementing-user-table-potential-feature/6266
>> ).
>>
>> Christoph
>>
>>>
>>>
>>> --
>>> *Thank you*
>>> *Warm Regards*
>>> Gangotree Rai
>>> PhD | Chemical Engineering
>>> Macromolecular Modeling and Simulation Laboratory
>>> Indian Institute of Technology Madras (IITM)
>>> Chennai 600036, Tamil Nadu, India
>>> Ph: (O) +91-731-857-5569 (Call) | +91-876-574-7978 (w)
>>>
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>>> 09:02:49 AM
>>>
>>
>>
>> --
>> Christoph Junghans
>> Web: http://www.compphys.de
>>
>

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[votca] Re: Votca compatibility in GROMACS

[Christoph Junghans]

On Sat, Jun 17, 2023 at 9:38 PM Gangotree Rai 
wrote:

> Dear Sir,
> I am new to this VOTCA field and am trying to learn through the VOTCA
> manual and its tutorial. My basic doubt is whether I can use VOTCA in the
> GROMACS 2020 version or not since VOTCA simulations are carried out with
> the tabulated function (potential). If not, then please suggest which
> GROMACS version is compatible with VOTCA.
>
You need to use gromacs-2019! gromacs-2020 dropped the tabulated potential
feature and it hasn't been re-implemented since (see
https://gitlab.com/gromacs/gromacs/-/issues/1347 and
https://gromacs.bioexcel.eu/t/reimplementing-user-table-potential-feature/6266
).

Christoph

>
>
> --
> *Thank you*
> *Warm Regards*
> Gangotree Rai
> PhD | Chemical Engineering
> Macromolecular Modeling and Simulation Laboratory
> Indian Institute of Technology Madras (IITM)
> Chennai 600036, Tamil Nadu, India
> Ph: (O) +91-731-857-5569 (Call) | +91-876-574-7978 (w)
>
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>


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Re: [votca] Question on the error of the FM

[Christoph Junghans]

On Fri, Jun 16, 2023 at 4:21 AM Cecília Álvares
 wrote:
>
> Hello,
>
> I understand that in the .force output files that are generated by VOTCA 
> after force-matching the third column is the force error (including the 
> block-averaging procedure, in case more I am using several 
> overdetermined-systems of equations).
>
> I was wondering exactly these errors are (mathematically speaking). I mean, 
> how do they the value of (F_il,model - Fil,ref)^2, which should ideally be 0, 
> at each point?

I guess if you would have an infinitely long trajectory and hence
infinitely long blocks the ends should go to 0.
We implemented this after https://doi.org/10.1007/978-94-010-0173-1_7,
so you can have a look at that as well.

>
> Also, if it is not much to ask, would someone have ready-to-go the magnitude 
> ( +/- ) of these errors in the force-fields derived via FM for propane in the 
> original VOTCA publication? ( https://doi.org/10.1021/ct900369w) I know I can 
> run this myself and check, so it is just in case someone happens to have this 
> information readily. It would be quite helpful. I am asking just to have a 
> reference on how small these errors should be: I want to be sure that the 
> values in my case are not too large (which would indicate that maybe my 
> system is not well described by pairwise potentials for example). Given that 
> the FM force-fields for hexane look quite beautiful, I wanted to use the 
> underlying error magnitude in the potential as a "reference" of how large 
> they should be.

The paper is from 2009, let me see if I can still find it. Please send
me your github username in an email.

Christoph

>
> Thanks a lot!
> Cecilia
>
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Re: [votca] Regarding-Getting-itp-files:

[Christoph Junghans]

On Wed, Jun 14, 2023, 22:55 Kankana Bhattacharjee <
kankanabhattacharje...@gmail.com> wrote:

> Sir, now angle_a1.xvg worked for gmx mdrun option.
>
What did you change?

I would like to know, if I run vacuum, single atomistic propane and single
> CG propane, all atom propane in vacuum then should I have to use "sd"
> integrator in all cases ?
>
You need some simulation that produces NVT ensemble, so the "sd" integrator
is one opinion or you could use "md" and an thermostat.

Christoph

>
>
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>  06/15/23,
> 10:21:58 AM
>
> On Thu, Jun 15, 2023 at 4:32 AM Christoph Junghans 
> wrote:
>
>>
>>
>> On Wed, Jun 14, 2023, 00:17 Kankana Bhattacharjee <
>> kankanabhattacharje...@gmail.com> wrote:
>>
>>> Dear Sir,
>>>
>>> All the table.xvg files (table_b1.xvg, table_b2.xvg, table_a1.xvg) are
>>> prepared using csg_call command. Now, I am trying to perform Gromacs CG-MD
>>> simulation of single CG propane using GROMACS and executed the
>>> command line:
>>>
>>>1.
>>>
>>>gmx_mpi mdrun -v -deffnm cg -tableb table_b1.xvg table_b2.xvg
>>>table_a1.xvg
>>>
>>>
>>>
>>> *Now, error is coming like this: *In table file 'table_a1.xvg' the x
>>> values are not equally spaced: 0.00
>>>
>>> 0.229153 0.343730
>>>
>>> How can I fix this issue i.e, equally spacing x values ?
>>>
>> I am not a 100 percent sure, what is going on!
>> Can you post the input files (pot and xvg) for the angle interaction?
>>
>> Christoph
>>
>>>
>>>
>>>
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>>>  06/14/23,
>>> 11:46:13 AM
>>>
>>> On Mon, Jun 12, 2023 at 5:55 PM Christoph Junghans 
>>> wrote:
>>>
>>>>
>>>>
>>>> On Mon, Jun 12, 2023, 03:37 Kankana Bhattacharjee <
>>>> kankanabhattacharje...@gmail.com> wrote:
>>>>
>>>>> And, sir while using the csg_call command for single propane, then
>>>>> what settings.xml file has to be used to convert into table.xvg format ?
>>>>> Because for single propane folder, there is no settings.xml file.
>>>>>
>>>> The settings file is just a simple file that contains some more
>>>> information about the interaction, this file should work:
>>>>
>>>> https://github.com/votca/votca/blob/master/csg-tutorials/propane/ibi/settings.xml
>>>>
>>>> When you run csg_call it will tell you which items are read.
>>>>
>>>>
>>>>>
>>>>>
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>>>>>  06/12/23,
>>>>> 03:03:46 PM
>>>>>
>>>>> On Mon, Jun 12, 2023 at 3:00 PM Kankana Bhattacharjee <
>>>>> kankanabhattacharje...@gmail.com> wrote:
>>>>>
>>>>>> Ok. Thanks a lot sir. But, what would be the maximum value for
>>>>>> specifying grid in case of bonds ?
>>>>>>
>>>>>>
>>>>>>
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>>>>>>  06/12/23,
>>>>>> 02:59:32 PM
>>>>>>
>>>>>> On Mon, Jun 12, 2023 at 8:09 AM Christoph Junghans <
>>>>>> jungh...@votca.org> wrote:
>>>>>>
>>>>>>>
>>>>>>

Re: [votca] Regarding-Getting-itp-files:

[Christoph Junghans]

On Mon, Jun 12, 2023, 03:37 Kankana Bhattacharjee <
kankanabhattacharje...@gmail.com> wrote:

> And, sir while using the csg_call command for single propane, then what
> settings.xml file has to be used to convert into table.xvg format ? Because
> for single propane folder, there is no settings.xml file.
>
The settings file is just a simple file that contains some more information
about the interaction, this file should work:
https://github.com/votca/votca/blob/master/csg-tutorials/propane/ibi/settings.xml

When you run csg_call it will tell you which items are read.


>
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>
> On Mon, Jun 12, 2023 at 3:00 PM Kankana Bhattacharjee <
> kankanabhattacharje...@gmail.com> wrote:
>
>> Ok. Thanks a lot sir. But, what would be the maximum value for specifying
>> grid in case of bonds ?
>>
>>
>>
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>>
>> On Mon, Jun 12, 2023 at 8:09 AM Christoph Junghans 
>> wrote:
>>
>>>
>>>
>>> On Fri, Jun 9, 2023 at 5:29 AM Kankana Bhattacharjee <
>>> kankanabhattacharje...@gmail.com> wrote:
>>>
>>>> Sir, I am not understanding the Resampling and extrapolation steps for
>>>> getting bonded.xvg files. For resampling options, in the command line:
>>>>   csg_resample --in table.pot --out table_resample.pot \ --grid
>>>> min:step:max
>>>>
>>>> How to choose min, step and max values here ? Kindly help me with
>>>> this.
>>>>
>>> There are some conditions that gromacs wants:
>>> - bonds type need to start at 0 to max (in nm)
>>> - angle type need to from 0 to 180 degrees
>>> - dihedrals type need to go from -18o t0 180 degrees
>>> (VOTCA internally uses radians, so you will need to convert that)
>>>
>>> Most of that is implemented in:
>>>
>>> https://github.com/votca/votca/blob/master/csg/share/scripts/inverse/potential_to_gromacs.sh
>>>
>>> You can actually try to use that with:
>>> $ csg_call --ia-type bond --ia-name bond1 --settings.xml table.xml
>>> convert_potential gromacs table.pot table.xvg
>>>
>>> Also see: https://www.votca.org/csg/preparing.html#exporting-the-table
>>>
>>> Christoph
>>>
>>>>
>>>>
>>>>
>>>>
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>>>>  06/09/23,
>>>> 04:58:12 PM
>>>>
>>>> On Fri, Jun 9, 2023 at 4:05 PM Kankana Bhattacharjee <
>>>> kankanabhattacharje...@gmail.com> wrote:
>>>>
>>>>> Dear Sir,
>>>>>
>>>>> When converting the Boltzmann inverted potential (angle.pot.ib) into
>>>>> table.xvg using the command line : *csg_call --ia-type angle
>>>>> --ia-name angle1 --options table_a1.xml \ convert_potential gromacs
>>>>> angle_rad.pot.ib table_a1.xvg*
>>>>> then, getting the error like this:
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> *table_linearop.pl <http://table_linearop.pl>: angle_rad.pot.ib to
>>>>> angle_rad.pot.scale.3tqbn with x' = 57.2957795*x + 0readin_table: Not
>>>>> enought columns in line 1 in file angle_rad.pot.ib, if you don't have 
>>>>> flags
>>>>> in your table add --sloppy-tables option to
>>>>> csg_callCallstack:/usr/bin/csg_call - linenumber 199do_external -
>>>>> lin

Re: [votca] Regarding-Getting-itp-files:

[Christoph Junghans]

On Mon, Jun 12, 2023, 03:30 Kankana Bhattacharjee <
kankanabhattacharje...@gmail.com> wrote:

> Ok. Thanks a lot sir. But, what would be the maximum value for specifying
> grid in case of bonds ?
>
That is system specific, you have make an educated guess how far the bonds
are stretched in the simulation.


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> 02:59:32 PM
>
> On Mon, Jun 12, 2023 at 8:09 AM Christoph Junghans 
> wrote:
>
>>
>>
>> On Fri, Jun 9, 2023 at 5:29 AM Kankana Bhattacharjee <
>> kankanabhattacharje...@gmail.com> wrote:
>>
>>> Sir, I am not understanding the Resampling and extrapolation steps for
>>> getting bonded.xvg files. For resampling options, in the command line:
>>>   csg_resample --in table.pot --out table_resample.pot \ --grid
>>> min:step:max
>>>
>>> How to choose min, step and max values here ? Kindly help me with this.
>>>
>>>
>> There are some conditions that gromacs wants:
>> - bonds type need to start at 0 to max (in nm)
>> - angle type need to from 0 to 180 degrees
>> - dihedrals type need to go from -18o t0 180 degrees
>> (VOTCA internally uses radians, so you will need to convert that)
>>
>> Most of that is implemented in:
>>
>> https://github.com/votca/votca/blob/master/csg/share/scripts/inverse/potential_to_gromacs.sh
>>
>> You can actually try to use that with:
>> $ csg_call --ia-type bond --ia-name bond1 --settings.xml table.xml
>> convert_potential gromacs table.pot table.xvg
>>
>> Also see: https://www.votca.org/csg/preparing.html#exporting-the-table
>>
>> Christoph
>>
>>>
>>>
>>>
>>>
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>>>  06/09/23,
>>> 04:58:12 PM
>>>
>>> On Fri, Jun 9, 2023 at 4:05 PM Kankana Bhattacharjee <
>>> kankanabhattacharje...@gmail.com> wrote:
>>>
>>>> Dear Sir,
>>>>
>>>> When converting the Boltzmann inverted potential (angle.pot.ib) into
>>>> table.xvg using the command line : *csg_call --ia-type angle --ia-name
>>>> angle1 --options table_a1.xml \ convert_potential gromacs angle_rad.pot.ib
>>>> table_a1.xvg*
>>>> then, getting the error like this:
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> *table_linearop.pl <http://table_linearop.pl>: angle_rad.pot.ib to
>>>> angle_rad.pot.scale.3tqbn with x' = 57.2957795*x + 0readin_table: Not
>>>> enought columns in line 1 in file angle_rad.pot.ib, if you don't have flags
>>>> in your table add --sloppy-tables option to
>>>> csg_callCallstack:/usr/bin/csg_call - linenumber 199do_external -
>>>> linenumber 176 in /usr/share/votca/scripts/inverse/functions_common.sh
>>>>   /usr/share/votca/scripts/inverse/potential_to_gromacs.sh - linenumber
>>>> 124do_external - linenumber 22 (see 'csg_call --cat function
>>>> do_external')die - linenumber 2 (see 'csg_call --cat
>>>> function
>>>> die')##
>>>>
>>>>   ## ERROR:
>>>>
>>>>## do_external: subscript
>>>>  ##
>>>> /usr/share/votca/scripts/inverse/table_linearop.pl
>>>> <http://table_linearop.pl> --on-x angle_rad.pot.ib
>>>> angle_rad.pot.scale.3tqbn 57.2957795 0 ## (from tags table linearop) failed
>>>>
>>>> ## Details can be found above
>>>>  ##
>>>>
>>>>
>>>> ###

Re: [votca] Regarding-Getting-itp-files:

[Christoph Junghans]

On Thu, Jun 8, 2023, 06:29 Kankana Bhattacharjee <
kankanabhattacharje...@gmail.com> wrote:

> Sorry sir, bonded section is also there. To obtain a bond table, the used
> command line is:
>
> csg_call --ia-type bond --ia-name XXX --options table.xml \
> convert_potential gromacs table_extrapolate.pot table.xvg
>
> I would like to know, in --ia-name flag, what I should I put there, would
> it foolow the name which is mentioned in the propane.xml file in bonded
> section (bond1, bond2) ?
>
Yes, it is just the same names you defined in table.xml.

Christoph

>
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>  06/08/23,
> 03:57:07 PM
>
> On Thu, Jun 8, 2023 at 3:46 PM Kankana Bhattacharjee <
> kankanabhattacharje...@gmail.com> wrote:
>
>> But, sir for this process, a table.xml file is given for non-bonded
>> intercations. But, how to do the same job for bonded distributions ?
>>
>>
>>
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>>  06/08/23,
>> 03:44:48 PM
>>
>> On Thu, Jun 8, 2023 at 3:42 PM Christoph Junghans 
>> wrote:
>>
>>>
>>>
>>> On Thu, Jun 8, 2023, 06:01 Kankana Bhattacharjee <
>>> kankanabhattacharje...@gmail.com> wrote:
>>>
>>>> Ok. Thank you sir. I understood that, table number concept i.e,
>>>> table_a1.xvg, table_b1.xvg. But, how can one generate those files to supply
>>>> in bonded.itp file ? I can see those table (bond1, angle1).xvg files in the
>>>> ibi directory. But, how those files get generated ?
>>>>
>>> https://www.votca.org/csg/preparing.html#exporting-the-table
>>>
>>>
>>>> -- Forwarded message -
>>>> From: Christoph Junghans 
>>>> Date: Thu, Jun 8, 2023 at 3:27 PM
>>>> Subject: Re: [votca] Regarding-Getting-itp-files:
>>>> To: Kankana Bhattacharjee 
>>>>
>>>>
>>>>
>>>>
>>>> On Thu, Jun 8, 2023, 01:43 Kankana Bhattacharjee <
>>>> kankanabhattacharje...@gmail.com> wrote:
>>>>
>>>>> Dear Sir,
>>>>>
>>>>> I would like to know, how in the case of CG propane.itp file, I have
>>>>> found that, "func type 8" is used which is tabulated functional form. And,
>>>>> in the case of "func type 8", there are two parameters "table number" and
>>>>> "spring constant" values. And, how two parameters (table number, spring
>>>>> constant) are obtained (which is equal to 1 in topol.top file) ? Like, as 
>>>>> I
>>>>> am doing it manually, and bonded values obtained from BI method, then how
>>>>> can I mention spring constant, and table number values in bonded.itp file 
>>>>> ?
>>>>>
>>>> The spring constant is yet another number the table gets multipled
>>>> with, but for BI you don't need another factor that hence we set it to 1.0!
>>>>
>>>> The table number is arbitrary, but needs to consistent with the files
>>>> name, table_b<#>.xvg and table_a<#>.xvg. (b for bond, a for angle, see the
>>>> Gromacs manual for details).
>>>>
>>>> Christoph
>>>>
>>>>>
>>>>> Thanks and regards
>>>>> Kankana Bhattacharjee
>>>>>
>>>>>
>>>>>
>>>>> [image: Mailtrack]
>>>>> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>>>>>  Sender
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>>>>>  06/08/23,
>>>>> 11:08:09 AM
>>>>>
>>>>> On Mon, Jun 5, 2023 at 7:13 PM Kankana Bhattacharjee <
>>>>> kankanabhattacharje...@gmail.com> wrote:
>>>>>
>>>>>> Ok sir
>>>>>>
>>>>>> On Mon, Jun 5, 2023, 19:00 Christoph Junghans 
>>>&g

Re: [votca] Regarding-Getting-itp-files:

[Christoph Junghans]

On Mon, Jun 5, 2023 at 7:11 AM Kankana Bhattacharjee <
kankanabhattacharje...@gmail.com> wrote:

> Ok sir.
> If i use CG MD only using gromacs without using votca, is it possible to
> do with gromacs 2020 or later version? If i don't use iterative methods
>
Well even the non-iterative methods like Boltzmann inversion and Force
Matching use tables.
You would have to fit them to a Lennard-Jones form to use Gromacs 2020.

Christoph

>
> On Mon, Jun 5, 2023, 18:16 Christoph Junghans  wrote:
>
>>
>>
>> On Mon, Jun 5, 2023 at 6:35 AM Kankana Bhattacharjee <
>> kankanabhattacharje...@gmail.com> wrote:
>>
>>> Ok sir. What should I do to fix it ?
>>>
>> Build VOTCA against gromacs-2019. VOTCA even has an option to build its
>> own gromacs (BUILD_OWN_GROMACS).
>>
>>
>>> Is it true for all iterative methods ?
>>>
>> Yes, but of course you can always use lammps to do the CG MD.
>>
>> Christoph
>>
>>
>>>
>>>
>>>
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>>>  06/05/23,
>>> 06:05:14 PM
>>>
>>> On Mon, Jun 5, 2023 at 6:04 PM Christoph Junghans 
>>> wrote:
>>>
>>>>
>>>>
>>>> On Mon, Jun 5, 2023 at 6:17 AM Kankana Bhattacharjee <
>>>> kankanabhattacharje...@gmail.com> wrote:
>>>>
>>>>> Dear Sir,
>>>>>
>>>>> This is the Fatal error obtained from inverse.log file:
>>>>>
>>>>>
>>>>>
>>>>> *Fatal error:The group cutoff scheme has been removed since GROMACS
>>>>> 2020. Please use theVerlet cutoff scheme.*
>>>>>
>>>> That is right to use tabulated interactions you will to use gromacs
>>>> 2019 (or lammps).
>>>>
>>>> VOTCA also prints a warning about that issue then you build it.
>>>> Status of tables in newer gromacs versions here:
>>>> https://gitlab.com/gromacs/gromacs/-/issues/1347, but
>>>> unfortunately not much has moved.
>>>>
>>>> Christoph
>>>>
>>>>
>>>>>
>>>>> Thanks & Regards
>>>>> Kankana Bhattacharjee
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> [image: Mailtrack]
>>>>> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>>>>>  Sender
>>>>> notified by
>>>>> Mailtrack
>>>>> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>>>>>  06/05/23,
>>>>> 05:46:29 PM
>>>>>
>>>>> On Mon, Jun 5, 2023 at 5:32 PM Christoph Junghans 
>>>>> wrote:
>>>>>
>>>>>>
>>>>>>
>>>>>> On Sun, Jun 4, 2023, 23:15 Kankana Bhattacharjee <
>>>>>> kankanabhattacharje...@gmail.com> wrote:
>>>>>>
>>>>>>> Dear Sir,
>>>>>>>
>>>>>>> RDF for A-A, B-B, A-B computed from atomistic simulation using
>>>>>>> csg_stat tool. Now, I am doing ibi method. But, error is coming during 
>>>>>>> step
>>>>>>> 1 like this:
>>>>>>> Appending to existing logfile inverse.log
>>>>>>> We are doing Method: ibi
>>>>>>> step 0 is already done - skipping
>>>>>>> Doing iteration 1 (dir step_001)
>>>>>>> Simulation with gromacs
>>>>>>> Automatically added 'cutoff-scheme = Group' to grompp.mdp, tabulated
>>>>>>> interactions only work with Group cutoff-scheme!
>>>>>>>
>>>>>>> ##
>>>>>>> #
>>>>>>>  #
>>>>>>> # ERROR:
>>>>>>> #
>>>>>>> # critical: 'gmx grompp -n index.ndx -f grompp.mdp -p topol.top -o
>>>>>>> topol.tpr -c conf.gro' failed  

Re: [votca] Re: VOTCA in homebrew

[Christoph Junghans]

On Mon, Jun 5, 2023 at 4:21 AM Cecília Álvares
 wrote:
>
> Be careful with the alcoholic tendencies! (joking haha)

Haha!

But thanks to all for helping out! VOTCA is available through homebrew now!

Christoph
>
> Em segunda-feira, 22 de maio de 2023 às 20:16:01 UTC+2, Christoph Junghans 
> escreveu:
>>
>> Hi users,
>>
>> We are in the process of getting VOTCA into homebrew, but we are missing a 
>> couple of GitHub stats!
>>
>> So if you would like to see VOTCA in homebrew, please fork, star AND watch 
>> the VOTCA repository on GitHub: https://github.com/votca/votca
>>
>> Thanks,
>>
>> Christoph
>
> --
> Join us on Slack: https://join.slack.com/t/votca/signup
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-- 
Christoph Junghans
Web: http://www.compphys.de

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Re: [votca] Regarding-Getting-itp-files:

[Christoph Junghans]

On Mon, Jun 5, 2023 at 6:17 AM Kankana Bhattacharjee <
kankanabhattacharje...@gmail.com> wrote:

> Dear Sir,
>
> This is the Fatal error obtained from inverse.log file:
>
>
>
> *Fatal error:The group cutoff scheme has been removed since GROMACS 2020.
> Please use theVerlet cutoff scheme.*
>
That is right to use tabulated interactions you will to use gromacs 2019
(or lammps).

VOTCA also prints a warning about that issue then you build it.
Status of tables in newer gromacs versions here:
https://gitlab.com/gromacs/gromacs/-/issues/1347, but unfortunately not
much has moved.

Christoph


>
> Thanks & Regards
> Kankana Bhattacharjee
>
>
>
>
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> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>  Sender
> notified by
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>  06/05/23,
> 05:46:29 PM
>
> On Mon, Jun 5, 2023 at 5:32 PM Christoph Junghans 
> wrote:
>
>>
>>
>> On Sun, Jun 4, 2023, 23:15 Kankana Bhattacharjee <
>> kankanabhattacharje...@gmail.com> wrote:
>>
>>> Dear Sir,
>>>
>>> RDF for A-A, B-B, A-B computed from atomistic simulation using csg_stat
>>> tool. Now, I am doing ibi method. But, error is coming during step 1 like
>>> this:
>>> Appending to existing logfile inverse.log
>>> We are doing Method: ibi
>>> step 0 is already done - skipping
>>> Doing iteration 1 (dir step_001)
>>> Simulation with gromacs
>>> Automatically added 'cutoff-scheme = Group' to grompp.mdp, tabulated
>>> interactions only work with Group cutoff-scheme!
>>>
>>> ##
>>> #
>>>  #
>>> # ERROR:
>>> #
>>> # critical: 'gmx grompp -n index.ndx -f grompp.mdp -p topol.top -o
>>> topol.tpr -c conf.gro' failed #
>>> # For details see the logfile
>>> /mnt/c/Users/KANKANA/Downloads/votca/csg-tutorials/propane/ibi-kankana/inverse.log
>>> #
>>>
>>
>> Please look up and post the detailed error message from inverse.log.
>>
>>
>> #
>>>#
>>>
>>> ##
>>> Terminated
>>>
>>> Kindly help me with this.
>>>
>>> Thanks & Regards
>>> kankana Bhattacharjee
>>>
>>>
>>>
>>>
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>>> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>>>  Sender
>>> notified by
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>>>  06/05/23,
>>> 10:44:51 AM
>>>
>>> On Sat, Jun 3, 2023 at 8:42 PM Christoph Junghans 
>>> wrote:
>>>
>>>>
>>>>
>>>> On Sat, Jun 3, 2023 at 9:00 AM Kankana Bhattacharjee <
>>>> kankanabhattacharje...@gmail.com> wrote:
>>>>
>>>>> Thank you sir. But IBI would be for multiple propane molecules. Isn't
>>>>> it ? It won't be for single propane i think
>>>>>
>>>> Yes, IBI (and IMC and RE) are for multiple molecules.
>>>>
>>>>
>>>>>
>>>>> On Sat, Jun 3, 2023, 19:47 Christoph Junghans 
>>>>> wrote:
>>>>>
>>>>>>
>>>>>>
>>>>>> On Sat, Jun 3, 2023 at 3:16 AM Kankana Bhattacharjee <
>>>>>> kankanabhattacharje...@gmail.com> wrote:
>>>>>>
>>>>>>> Sir, i performed atomistic simulation of single  propane in vaccum.
>>>>>>> But, if we use multiple propane simulation in vaccum, then csg_stat can
>>>>>>> give RDF which can be compared with RDF of ibi/imc methods ?
>>>>>>>
>>>>>> The single molecule in vacuum is a common separation strategy to
>>>>>> determine the intertra molecular interactions. In short get the bonded
>>>>>> interactions from BI for the single chain run and then run IBI for the
>>>>>> non-bonded interactions.
>>>>>> see the Tschoep paper from 1998 (
>>>>>> https://www.votca.or

Re: [votca] Regarding-Getting-itp-files:

[Christoph Junghans]

On Sun, Jun 4, 2023, 23:15 Kankana Bhattacharjee <
kankanabhattacharje...@gmail.com> wrote:

> Dear Sir,
>
> RDF for A-A, B-B, A-B computed from atomistic simulation using csg_stat
> tool. Now, I am doing ibi method. But, error is coming during step 1 like
> this:
> Appending to existing logfile inverse.log
> We are doing Method: ibi
> step 0 is already done - skipping
> Doing iteration 1 (dir step_001)
> Simulation with gromacs
> Automatically added 'cutoff-scheme = Group' to grompp.mdp, tabulated
> interactions only work with Group cutoff-scheme!
>
> ##
> #
>#
> # ERROR:
>   #
> # critical: 'gmx grompp -n index.ndx -f grompp.mdp -p topol.top -o
> topol.tpr -c conf.gro' failed #
> # For details see the logfile
> /mnt/c/Users/KANKANA/Downloads/votca/csg-tutorials/propane/ibi-kankana/inverse.log
> #
>

Please look up and post the detailed error message from inverse.log.


#
>  #
>
> ##
> Terminated
>
> Kindly help me with this.
>
> Thanks & Regards
> kankana Bhattacharjee
>
>
>
>
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> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>  Sender
> notified by
> Mailtrack
> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>  06/05/23,
> 10:44:51 AM
>
> On Sat, Jun 3, 2023 at 8:42 PM Christoph Junghans 
> wrote:
>
>>
>>
>> On Sat, Jun 3, 2023 at 9:00 AM Kankana Bhattacharjee <
>> kankanabhattacharje...@gmail.com> wrote:
>>
>>> Thank you sir. But IBI would be for multiple propane molecules. Isn't it
>>> ? It won't be for single propane i think
>>>
>> Yes, IBI (and IMC and RE) are for multiple molecules.
>>
>>
>>>
>>> On Sat, Jun 3, 2023, 19:47 Christoph Junghans 
>>> wrote:
>>>
>>>>
>>>>
>>>> On Sat, Jun 3, 2023 at 3:16 AM Kankana Bhattacharjee <
>>>> kankanabhattacharje...@gmail.com> wrote:
>>>>
>>>>> Sir, i performed atomistic simulation of single  propane in vaccum.
>>>>> But, if we use multiple propane simulation in vaccum, then csg_stat can
>>>>> give RDF which can be compared with RDF of ibi/imc methods ?
>>>>>
>>>> The single molecule in vacuum is a common separation strategy to
>>>> determine the intertra molecular interactions. In short get the bonded
>>>> interactions from BI for the single chain run and then run IBI for the
>>>> non-bonded interactions.
>>>> see the Tschoep paper from 1998 (
>>>> https://www.votca.org/csg/bibliography.html#tschoep-1998)
>>>>
>>>> I want to know how to choose which method (ibi, imc) would be accurate
>>>>> to give accurate structural properties?
>>>>>
>>>> That depends on the system. IBI, IMC & Re are all structure-based
>>>> methods and try to reproduce the structure.
>>>> Usually IBI is more robust, but needs more iterations. But IMC
>>>> converges faster, but needs longer iterations. Marvin (who is on the
>>>> mailing list as well) wrote an interesting paper about that recently:
>>>> https://doi.org/10.1021/acs.jctc.2c00665
>>>>
>>>>
>>>>> On Sat, Jun 3, 2023, 09:48 Kankana Bhattacharjee <
>>>>> kankanabhattacharje...@gmail.com> wrote:
>>>>>
>>>>>> Sir, actually it was given by professor so that, for any arbitrary
>>>>>> molecule also I can make itp file to run CG-MD simulation. It is just for
>>>>>> my learning purpose.
>>>>>>
>>>>>> Suppose, in the tutorial for CG systems topol.top file is there. Like
>>>>>> for ibi, imc method etc. topol.top is there. But, for any unknown organic
>>>>>> CG molecule how can one generate itp file to run CGMD simulation ?
>>>>>>
>>>>>>
>>>>>>
>>>>>> [image: Mailtrack]
>>>>>> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>>>>>>  Sender
>>>>>> notified by
>>>>>> Mailtrack
>>>>>> <https

Re: [votca] Regarding-Getting-itp-files:

[Christoph Junghans]

On Sat, Jun 3, 2023 at 9:00 AM Kankana Bhattacharjee <
kankanabhattacharje...@gmail.com> wrote:

> Thank you sir. But IBI would be for multiple propane molecules. Isn't it ?
> It won't be for single propane i think
>
Yes, IBI (and IMC and RE) are for multiple molecules.


>
> On Sat, Jun 3, 2023, 19:47 Christoph Junghans  wrote:
>
>>
>>
>> On Sat, Jun 3, 2023 at 3:16 AM Kankana Bhattacharjee <
>> kankanabhattacharje...@gmail.com> wrote:
>>
>>> Sir, i performed atomistic simulation of single  propane in vaccum. But,
>>> if we use multiple propane simulation in vaccum, then csg_stat can give RDF
>>> which can be compared with RDF of ibi/imc methods ?
>>>
>> The single molecule in vacuum is a common separation strategy to
>> determine the intertra molecular interactions. In short get the bonded
>> interactions from BI for the single chain run and then run IBI for the
>> non-bonded interactions.
>> see the Tschoep paper from 1998 (
>> https://www.votca.org/csg/bibliography.html#tschoep-1998)
>>
>> I want to know how to choose which method (ibi, imc) would be accurate to
>>> give accurate structural properties?
>>>
>> That depends on the system. IBI, IMC & Re are all structure-based methods
>> and try to reproduce the structure.
>> Usually IBI is more robust, but needs more iterations. But IMC converges
>> faster, but needs longer iterations. Marvin (who is on the mailing list as
>> well) wrote an interesting paper about that recently:
>> https://doi.org/10.1021/acs.jctc.2c00665
>>
>>
>>> On Sat, Jun 3, 2023, 09:48 Kankana Bhattacharjee <
>>> kankanabhattacharje...@gmail.com> wrote:
>>>
>>>> Sir, actually it was given by professor so that, for any arbitrary
>>>> molecule also I can make itp file to run CG-MD simulation. It is just for
>>>> my learning purpose.
>>>>
>>>> Suppose, in the tutorial for CG systems topol.top file is there. Like
>>>> for ibi, imc method etc. topol.top is there. But, for any unknown organic
>>>> CG molecule how can one generate itp file to run CGMD simulation ?
>>>>
>>>>
>>>>
>>>> [image: Mailtrack]
>>>> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>>>>  Sender
>>>> notified by
>>>> Mailtrack
>>>> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>>>>  06/03/23,
>>>> 09:45:05 AM
>>>>
>>>> On Sat, Jun 3, 2023 at 9:42 AM Christoph Junghans 
>>>> wrote:
>>>>
>>>>>
>>>>>
>>>>> On Fri, Jun 2, 2023 at 21:00 Kankana Bhattacharjee <
>>>>> kankanabhattacharje...@gmail.com> wrote:
>>>>>
>>>>>> Actually sir, it was asked me to prepare propane.itp (for CG).
>>>>>>
>>>>> Sorry, can you explain a bit more why you need an itp file? All the
>>>>> files (except for the potentials) are in the tutorial already.
>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> [image: Mailtrack]
>>>>>> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>>>>>>  Sender
>>>>>> notified by
>>>>>> Mailtrack
>>>>>> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>>>>>>  06/03/23,
>>>>>> 08:29:51 AM
>>>>>>
>>>>>> On Sat, Jun 3, 2023 at 4:15 AM Christoph Junghans 
>>>>>> wrote:
>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Fri, Jun 2, 2023 at 12:34 PM Kankana Bhattacharjee <
>>>>>>> kankanabhattacharje...@gmail.com> wrote:
>>>>>>>
>>>>>>>>
>>>>>>>> Dear Sir,
>>>>>>>>
>>>>>>>> I have done boltzmann inversion of propane. now, for getting
>>>>>>>> nonbonded parameters what protocol should I follow ? Because, my aim 
>>>>>>>> is to
>>>>>>>> generate GROMACS compatible itp file for CG propane so that, can 
>>>>>>>> perform
>>>>>>>> CG-MD using Votca.
>>>>>>>>
>>>>>>> 

Re: [votca] Re: non-continuous domain interval for non-bonded interaction in force-matching

[Christoph Junghans]

On Wed, May 31, 2023 at 4:27 AM Cecília Álvares
 wrote:
>
> Hmm.. maybe this is actually a very stupid question, because, given that the 
> potential is built by using splines that hold within a small subinterval 
> defined in , I suppose I could get the same result by splitting the 
> ranges of non-zero RDF in different interactions. (it should give the same 
> results, right?)

The reason why we haven't implemented support for non-continuous
domains is mainly that it is complicated to get all the cases right
and so we thought one could just do a piecewise ibi and then combine
it.

Christoph

>
> Em quarta-feira, 31 de maio de 2023 às 12:07:35 UTC+2, Cecília Álvares 
> escreveu:
>>
>> (I mean, in this case, I could get "chops" of how the potential would look 
>> like in different intervals (corresponding to g(r) != 0) and I later can 
>> connected the different portions by doing some sort of interpolation myself.)
>>
>> Em quarta-feira, 31 de maio de 2023 às 11:54:18 UTC+2, Cecília Álvares 
>> escreveu:
>>>
>>> Hello everyone,
>>>
>>> I was wondering if there is a way to  define a "non-continuous" domain 
>>> interval when setting up the settings.xml file to do force-matching of 
>>> non-bonded potentials (for example) within VOTCA. I mean, in my case, since 
>>> I am deriving potentials for a xtalline solid, I have peaks in the RDF that 
>>> go up and down back to 0 (e.g. below), which would give rise to non-sampled 
>>> intervals for the potential if I was to use a continuous interval for rij 
>>> going from the first peak to the last.
>>>
>>>
> --
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-- 
Christoph Junghans
Web: http://www.compphys.de

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Re: [votca] Regarding-Getting-itp-files:

[Christoph Junghans]

On Sat, Jun 3, 2023 at 3:16 AM Kankana Bhattacharjee <
kankanabhattacharje...@gmail.com> wrote:

> Sir, i performed atomistic simulation of single  propane in vaccum. But,
> if we use multiple propane simulation in vaccum, then csg_stat can give RDF
> which can be compared with RDF of ibi/imc methods ?
>
The single molecule in vacuum is a common separation strategy to determine
the intertra molecular interactions. In short get the bonded interactions
from BI for the single chain run and then run IBI for the non-bonded
interactions.
see the Tschoep paper from 1998 (
https://www.votca.org/csg/bibliography.html#tschoep-1998)

I want to know how to choose which method (ibi, imc) would be accurate to
> give accurate structural properties?
>
That depends on the system. IBI, IMC & Re are all structure-based methods
and try to reproduce the structure.
Usually IBI is more robust, but needs more iterations. But IMC converges
faster, but needs longer iterations. Marvin (who is on the mailing list as
well) wrote an interesting paper about that recently:
https://doi.org/10.1021/acs.jctc.2c00665


> On Sat, Jun 3, 2023, 09:48 Kankana Bhattacharjee <
> kankanabhattacharje...@gmail.com> wrote:
>
>> Sir, actually it was given by professor so that, for any arbitrary
>> molecule also I can make itp file to run CG-MD simulation. It is just for
>> my learning purpose.
>>
>> Suppose, in the tutorial for CG systems topol.top file is there. Like for
>> ibi, imc method etc. topol.top is there. But, for any unknown organic CG
>> molecule how can one generate itp file to run CGMD simulation ?
>>
>>
>>
>> [image: Mailtrack]
>> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>>  Sender
>> notified by
>> Mailtrack
>> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>>  06/03/23,
>> 09:45:05 AM
>>
>> On Sat, Jun 3, 2023 at 9:42 AM Christoph Junghans 
>> wrote:
>>
>>>
>>>
>>> On Fri, Jun 2, 2023 at 21:00 Kankana Bhattacharjee <
>>> kankanabhattacharje...@gmail.com> wrote:
>>>
>>>> Actually sir, it was asked me to prepare propane.itp (for CG).
>>>>
>>> Sorry, can you explain a bit more why you need an itp file? All the
>>> files (except for the potentials) are in the tutorial already.
>>>
>>>>
>>>>
>>>>
>>>>
>>>> [image: Mailtrack]
>>>> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>>>>  Sender
>>>> notified by
>>>> Mailtrack
>>>> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>>>>  06/03/23,
>>>> 08:29:51 AM
>>>>
>>>> On Sat, Jun 3, 2023 at 4:15 AM Christoph Junghans 
>>>> wrote:
>>>>
>>>>>
>>>>>
>>>>> On Fri, Jun 2, 2023 at 12:34 PM Kankana Bhattacharjee <
>>>>> kankanabhattacharje...@gmail.com> wrote:
>>>>>
>>>>>>
>>>>>> Dear Sir,
>>>>>>
>>>>>> I have done boltzmann inversion of propane. now, for getting
>>>>>> nonbonded parameters what protocol should I follow ? Because, my aim is 
>>>>>> to
>>>>>> generate GROMACS compatible itp file for CG propane so that, can perform
>>>>>> CG-MD using Votca.
>>>>>>
>>>>> Why can't you use the topology files from the propane tutorial?
>>>>> https://github.com/votca/votca/tree/master/csg-tutorials/propane/ibi
>>>>> I am asking because most of the CG methods VOTCA implement work on
>>>>> tabulated potentials only.
>>>>>
>>>>> Christoph
>>>>>
>>>>>
>>>>>>
>>>>>> Thanks & Regards
>>>>>> Kankana Bhattacharjee
>>>>>>
>>>>>>
>>>>>> [image: Mailtrack]
>>>>>> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>>>>>>  Sender
>>>>>> notified by
>>>>>> Mailtrack
>>>>>> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>>>>>>  06/03/23,
>>>>>> 12:00:35 AM
>>>>>>
>>>>>> On Fri, Jun 2, 2023 at 9:13 PM Christoph Junghans 
>>>>>> wrote:
>>>

Re: [votca] Regarding-Getting-itp-files:

[Christoph Junghans]

On Fri, Jun 2, 2023 at 10:19 PM Kankana Bhattacharjee <
kankanabhattacharje...@gmail.com> wrote:

> Sir, actually it was given by professor so that, for any arbitrary
> molecule also I can make itp file to run CG-MD simulation. It is just for
> my learning purpose.
>
> Suppose, in the tutorial for CG systems topol.top file is there. Like for
> ibi, imc method etc. topol.top is there. But, for any unknown organic CG
> molecule how can one generate itp file to run CGMD simulation ?
>
Well the short answer is, you will have to write them by hand! csg_gmxtopol
can help as a starting point, but the rest you will have to do yourself.
Maybe there are tools for that, but that would be more a question for the
gromacs mailing list.

Christoph

>
>
> [image: Mailtrack]
> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>  Sender
> notified by
> Mailtrack
> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>  06/03/23,
> 09:45:05 AM
>
> On Sat, Jun 3, 2023 at 9:42 AM Christoph Junghans 
> wrote:
>
>>
>>
>> On Fri, Jun 2, 2023 at 21:00 Kankana Bhattacharjee <
>> kankanabhattacharje...@gmail.com> wrote:
>>
>>> Actually sir, it was asked me to prepare propane.itp (for CG).
>>>
>> Sorry, can you explain a bit more why you need an itp file? All the files
>> (except for the potentials) are in the tutorial already.
>>
>>>
>>>
>>>
>>>
>>> [image: Mailtrack]
>>> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>>>  Sender
>>> notified by
>>> Mailtrack
>>> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>>>  06/03/23,
>>> 08:29:51 AM
>>>
>>> On Sat, Jun 3, 2023 at 4:15 AM Christoph Junghans 
>>> wrote:
>>>
>>>>
>>>>
>>>> On Fri, Jun 2, 2023 at 12:34 PM Kankana Bhattacharjee <
>>>> kankanabhattacharje...@gmail.com> wrote:
>>>>
>>>>>
>>>>> Dear Sir,
>>>>>
>>>>> I have done boltzmann inversion of propane. now, for getting nonbonded
>>>>> parameters what protocol should I follow ? Because, my aim is to generate
>>>>> GROMACS compatible itp file for CG propane so that, can perform CG-MD 
>>>>> using
>>>>> Votca.
>>>>>
>>>> Why can't you use the topology files from the propane tutorial?
>>>> https://github.com/votca/votca/tree/master/csg-tutorials/propane/ibi
>>>> I am asking because most of the CG methods VOTCA implement work on
>>>> tabulated potentials only.
>>>>
>>>> Christoph
>>>>
>>>>
>>>>>
>>>>> Thanks & Regards
>>>>> Kankana Bhattacharjee
>>>>>
>>>>>
>>>>> [image: Mailtrack]
>>>>> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>>>>>  Sender
>>>>> notified by
>>>>> Mailtrack
>>>>> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>>>>>  06/03/23,
>>>>> 12:00:35 AM
>>>>>
>>>>> On Fri, Jun 2, 2023 at 9:13 PM Christoph Junghans 
>>>>> wrote:
>>>>>
>>>>>> Forgot to CC the mailing list, so here is the answer for others.
>>>>>>
>>>>>> -- Forwarded message -
>>>>>> From: Christoph Junghans 
>>>>>> Date: Fri, Jun 2, 2023 at 8:22 AM
>>>>>> Subject: Re: [votca] Regarding-Getting-itp-files:
>>>>>> To: Kankana Bhattacharjee 
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Fri, Jun 2, 2023 at 8:06 AM Kankana Bhattacharjee <
>>>>>> kankanabhattacharje...@gmail.com> wrote:
>>>>>>
>>>>>>> Sir, after boltzmann inversion, bond.dist.ib, angle.dist.ib and
>>>>>>> bond.pot.ib, angle.pot.ib (after using tab command)files generated. So,
>>>>>>> where will I get sigma, epsilon values
>>>>>>>
>>>>>>
>>>>>> I am not a 100% sure what you mean.
>>>>>>
>>>>>> When you use nbfunc=1 and comb-rule=1, the sigma and epsilon
>>>>>> column i

Re: [votca] Regarding-Getting-itp-files:

[Christoph Junghans]

On Fri, Jun 2, 2023 at 21:00 Kankana Bhattacharjee <
kankanabhattacharje...@gmail.com> wrote:

> Actually sir, it was asked me to prepare propane.itp (for CG).
>
Sorry, can you explain a bit more why you need an itp file? All the files
(except for the potentials) are in the tutorial already.

>
>
>
>
> [image: Mailtrack]
> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>  Sender
> notified by
> Mailtrack
> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>  06/03/23,
> 08:29:51 AM
>
> On Sat, Jun 3, 2023 at 4:15 AM Christoph Junghans 
> wrote:
>
>>
>>
>> On Fri, Jun 2, 2023 at 12:34 PM Kankana Bhattacharjee <
>> kankanabhattacharje...@gmail.com> wrote:
>>
>>>
>>> Dear Sir,
>>>
>>> I have done boltzmann inversion of propane. now, for getting nonbonded
>>> parameters what protocol should I follow ? Because, my aim is to generate
>>> GROMACS compatible itp file for CG propane so that, can perform CG-MD using
>>> Votca.
>>>
>> Why can't you use the topology files from the propane tutorial?
>> https://github.com/votca/votca/tree/master/csg-tutorials/propane/ibi
>> I am asking because most of the CG methods VOTCA implement work on
>> tabulated potentials only.
>>
>> Christoph
>>
>>
>>>
>>> Thanks & Regards
>>> Kankana Bhattacharjee
>>>
>>>
>>> [image: Mailtrack]
>>> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>>>  Sender
>>> notified by
>>> Mailtrack
>>> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>>>  06/03/23,
>>> 12:00:35 AM
>>>
>>> On Fri, Jun 2, 2023 at 9:13 PM Christoph Junghans 
>>> wrote:
>>>
>>>> Forgot to CC the mailing list, so here is the answer for others.
>>>>
>>>> -- Forwarded message -
>>>> From: Christoph Junghans 
>>>> Date: Fri, Jun 2, 2023 at 8:22 AM
>>>> Subject: Re: [votca] Regarding-Getting-itp-files:
>>>> To: Kankana Bhattacharjee 
>>>>
>>>>
>>>>
>>>>
>>>> On Fri, Jun 2, 2023 at 8:06 AM Kankana Bhattacharjee <
>>>> kankanabhattacharje...@gmail.com> wrote:
>>>>
>>>>> Sir, after boltzmann inversion, bond.dist.ib, angle.dist.ib and
>>>>> bond.pot.ib, angle.pot.ib (after using tab command)files generated. So,
>>>>> where will I get sigma, epsilon values
>>>>>
>>>>
>>>> I am not a 100% sure what you mean.
>>>>
>>>> When you use nbfunc=1 and comb-rule=1, the sigma and epsilon column in
>>>> the atomtypes block are actually the C6 and C12 parameters (i.e. the
>>>> prefactor of 1/r**6 and 1/r**12).
>>>> But if you then use tables (vdwtype = user in the mdp file), 1/r**6 and
>>>> 1/r**12 gets replaced with the function from files you provided (e.g.
>>>> obtained by boltzmann inversion) And hence in VOTCA we just set C6=C12=1,
>>>> so that the table is used unmodified.
>>>>
>>>> Hope that helps,
>>>>
>>>> Christoph
>>>>
>>>>
>>>>
>>>>
>>>>>
>>>>>
>>>>>
>>>>> [image: Mailtrack]
>>>>> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>>>>>  Sender
>>>>> notified by
>>>>> Mailtrack
>>>>> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>>>>>  06/02/23,
>>>>> 07:34:36 PM
>>>>>
>>>>> On Fri, Jun 2, 2023 at 7:27 PM Christoph Junghans 
>>>>> wrote:
>>>>>
>>>>>>
>>>>>>
>>>>>> On Fri, Jun 2, 2023 at 7:44 AM Kankana Bhattacharjee <
>>>>>> kankanabhattacharje...@gmail.com> wrote:
>>>>>>
>>>>>>> Sir, I would like to know how sigma, epsilon and default section was
>>>>>>> decided fpr CG-MD  simulation ?
>>>>>>>
>>>>>>
>>>>>> no sigma and epsilon, it is all tabulated interactions.
>>>>>> see
>>>>>>
>>>>>> https://github.com/votca/votca/blob/master/csg-t

Re: [votca] Regarding-Getting-itp-files:

[Christoph Junghans]

On Fri, Jun 2, 2023 at 12:34 PM Kankana Bhattacharjee <
kankanabhattacharje...@gmail.com> wrote:

>
> Dear Sir,
>
> I have done boltzmann inversion of propane. now, for getting nonbonded
> parameters what protocol should I follow ? Because, my aim is to generate
> GROMACS compatible itp file for CG propane so that, can perform CG-MD using
> Votca.
>
Why can't you use the topology files from the propane tutorial?
https://github.com/votca/votca/tree/master/csg-tutorials/propane/ibi
I am asking because most of the CG methods VOTCA implement work on
tabulated potentials only.

Christoph


>
> Thanks & Regards
> Kankana Bhattacharjee
>
>
> [image: Mailtrack]
> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>  Sender
> notified by
> Mailtrack
> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>  06/03/23,
> 12:00:35 AM
>
> On Fri, Jun 2, 2023 at 9:13 PM Christoph Junghans 
> wrote:
>
>> Forgot to CC the mailing list, so here is the answer for others.
>>
>> -- Forwarded message -
>> From: Christoph Junghans 
>> Date: Fri, Jun 2, 2023 at 8:22 AM
>> Subject: Re: [votca] Regarding-Getting-itp-files:
>> To: Kankana Bhattacharjee 
>>
>>
>>
>>
>> On Fri, Jun 2, 2023 at 8:06 AM Kankana Bhattacharjee <
>> kankanabhattacharje...@gmail.com> wrote:
>>
>>> Sir, after boltzmann inversion, bond.dist.ib, angle.dist.ib and
>>> bond.pot.ib, angle.pot.ib (after using tab command)files generated. So,
>>> where will I get sigma, epsilon values
>>>
>>
>> I am not a 100% sure what you mean.
>>
>> When you use nbfunc=1 and comb-rule=1, the sigma and epsilon column in
>> the atomtypes block are actually the C6 and C12 parameters (i.e. the
>> prefactor of 1/r**6 and 1/r**12).
>> But if you then use tables (vdwtype = user in the mdp file), 1/r**6 and
>> 1/r**12 gets replaced with the function from files you provided (e.g.
>> obtained by boltzmann inversion) And hence in VOTCA we just set C6=C12=1,
>> so that the table is used unmodified.
>>
>> Hope that helps,
>>
>> Christoph
>>
>>
>>
>>
>>>
>>>
>>>
>>> [image: Mailtrack]
>>> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>>>  Sender
>>> notified by
>>> Mailtrack
>>> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>>>  06/02/23,
>>> 07:34:36 PM
>>>
>>> On Fri, Jun 2, 2023 at 7:27 PM Christoph Junghans 
>>> wrote:
>>>
>>>>
>>>>
>>>> On Fri, Jun 2, 2023 at 7:44 AM Kankana Bhattacharjee <
>>>> kankanabhattacharje...@gmail.com> wrote:
>>>>
>>>>> Sir, I would like to know how sigma, epsilon and default section was
>>>>> decided fpr CG-MD  simulation ?
>>>>>
>>>>
>>>> no sigma and epsilon, it is all tabulated interactions.
>>>> see
>>>>
>>>> https://github.com/votca/votca/blob/master/csg-tutorials/hexane/ibi_nonbonded/grompp.mdp#L73
>>>>
>>>> and those tables you get from boltzmann inversion (or force matching).
>>>>
>>>> Christoph
>>>>
>>>>> -- Forwarded message -
>>>>> From: Christoph Junghans 
>>>>> Date: Fri, Jun 2, 2023 at 7:10 PM
>>>>> Subject: Re: [votca] Regarding-Getting-itp-files:
>>>>> To: Kankana Bhattacharjee 
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Fri, Jun 2, 2023 at 3:40 AM Kankana Bhattacharjee <
>>>>> kankanabhattacharje...@gmail.com> wrote:
>>>>>
>>>>>> Dear Sir,
>>>>>>
>>>>>> I would like to know that, in votca beads are defined using "A, B"
>>>>>> etc. But, how to understand what type of bead it is i.e, polar, aploar,
>>>>>> charged etc. Using A, B beads can anyone run GROMACS MD simulation ?
>>>>>>
>>>>>
>>>>> In the topol.top of the coarse grained simulation you can set the
>>>>> charge, e.g. see:
>>>>>
>>>>> https://github.com/votca/votca/blob/master/csg-tutorials/hexane/ibi_nonbonded/topol.top#L5_L8
>>>>>
>>>>>
>>>>> Christoph
>>>>>
>>>>>
>>&g

Fwd: [votca] Regarding-Getting-itp-files:

[Christoph Junghans]

Forgot to CC the mailing list, so here is the answer for others.

-- Forwarded message -
From: Christoph Junghans 
Date: Fri, Jun 2, 2023 at 8:22 AM
Subject: Re: [votca] Regarding-Getting-itp-files:
To: Kankana Bhattacharjee 




On Fri, Jun 2, 2023 at 8:06 AM Kankana Bhattacharjee <
kankanabhattacharje...@gmail.com> wrote:

> Sir, after boltzmann inversion, bond.dist.ib, angle.dist.ib and
> bond.pot.ib, angle.pot.ib (after using tab command)files generated. So,
> where will I get sigma, epsilon values
>

I am not a 100% sure what you mean.

When you use nbfunc=1 and comb-rule=1, the sigma and epsilon column in
the atomtypes block are actually the C6 and C12 parameters (i.e. the
prefactor of 1/r**6 and 1/r**12).
But if you then use tables (vdwtype = user in the mdp file), 1/r**6 and
1/r**12 gets replaced with the function from files you provided (e.g.
obtained by boltzmann inversion) And hence in VOTCA we just set C6=C12=1,
so that the table is used unmodified.

Hope that helps,

Christoph




>
>
>
> [image: Mailtrack]
> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>  Sender
> notified by
> Mailtrack
> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>  06/02/23,
> 07:34:36 PM
>
> On Fri, Jun 2, 2023 at 7:27 PM Christoph Junghans 
> wrote:
>
>>
>>
>> On Fri, Jun 2, 2023 at 7:44 AM Kankana Bhattacharjee <
>> kankanabhattacharje...@gmail.com> wrote:
>>
>>> Sir, I would like to know how sigma, epsilon and default section was
>>> decided fpr CG-MD  simulation ?
>>>
>>
>> no sigma and epsilon, it is all tabulated interactions.
>> see
>>
>> https://github.com/votca/votca/blob/master/csg-tutorials/hexane/ibi_nonbonded/grompp.mdp#L73
>>
>> and those tables you get from boltzmann inversion (or force matching).
>>
>> Christoph
>>
>>> -- Forwarded message -
>>> From: Christoph Junghans 
>>> Date: Fri, Jun 2, 2023 at 7:10 PM
>>> Subject: Re: [votca] Regarding-Getting-itp-files:
>>> To: Kankana Bhattacharjee 
>>>
>>>
>>>
>>>
>>> On Fri, Jun 2, 2023 at 3:40 AM Kankana Bhattacharjee <
>>> kankanabhattacharje...@gmail.com> wrote:
>>>
>>>> Dear Sir,
>>>>
>>>> I would like to know that, in votca beads are defined using "A, B" etc.
>>>> But, how to understand what type of bead it is i.e, polar, aploar, charged
>>>> etc. Using A, B beads can anyone run GROMACS MD simulation ?
>>>>
>>>
>>> In the topol.top of the coarse grained simulation you can set the
>>> charge, e.g. see:
>>>
>>> https://github.com/votca/votca/blob/master/csg-tutorials/hexane/ibi_nonbonded/topol.top#L5_L8
>>>
>>>
>>> Christoph
>>>
>>>
>>>> Thanks & Regards
>>>> Kankana Bhattacharjee
>>>>
>>>>
>>>>
>>>> [image: Mailtrack]
>>>> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>>>>  Sender
>>>> notified by
>>>> Mailtrack
>>>> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>>>>  06/02/23,
>>>> 03:05:36 PM
>>>>
>>>> On Fri, Jun 2, 2023 at 11:06 AM Kankana Bhattacharjee <
>>>> kankanabhattacharje...@gmail.com> wrote:
>>>>
>>>>> Dear Sir,
>>>>>
>>>>> I have included the individual bond section in propane.xml file. Now,
>>>>> distribution is generating.
>>>>> But, for getting non-bonded parameters, which procedure should I have
>>>>> to follow ? I can use either Force Matching or Iterative methods to get
>>>>> non-bonded parameters.
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> [image: Mailtrack]
>>>>> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>>>>>  Sender
>>>>> notified by
>>>>> Mailtrack
>>>>> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>>>>>  06/02/23,
>>>>> 11:03:20 AM
>>>>>
>>>>> On Fri, Jun 2, 2023 at 9:49 AM Kankana Bhattacharjee <
>>>>> kankanabhattacharje...@gmail.com> wrote:
>>>>>
>>>>>> Dear Sir,
&g

Re: [votca] Regarding-Getting-itp-files:

[Christoph Junghans]

On Thu, Jun 1, 2023 at 5:22 AM Kankana Bhattacharjee <
kankanabhattacharje...@gmail.com> wrote:

> Dear Sir,
>
> I am trying to generate the histogram of bonded distribution and convert
> into the boltzmann inverted potential for single propane which is given in
> the tutorial. Since, in case of CG propane two bond length is present
> (A1-B1 and B1-A2) which is mentioned in the propane.xml file and similarly
> one angle. So, I am not understanding how can I generate distribution of
> every bond of propane molecule. I have performed short 5 ps run of single
> propane molecule. When I am adding the line in boltzmann.cmds as:
> hist bond1.dist.ib *:bond1:*
> hist bond2.dist.ib *:bond2:*, then no plottable
> bond1.dist.ib/bond2.dist.ib is generating.
>
> If you don't want to average over the 2 bonds the easiest way to do that
is to add another bond block here:
https://github.com/votca/votca/blob/master/csg-tutorials/propane/atomistic/propane.xml#L34_L40

the names should be "bond1" and "bond2" for your application above.

And then run csg_stat (or csg_boltzmann):
https://github.com/votca/votca/blob/master/csg-tutorials/propane/atomistic/run.sh#L22

Christoph

There is

> My aim is to generate the every bond length histogram
> Please provide me the suggestions.
>
>
> Thanks & Regards
> Kankana Bhattacharjee
> Ph. D. Scholar
> Department of Chemistry
> Ashoka University
> Sonipat, Haryana
>
>
>
> [image: Mailtrack]
> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>  Sender
> notified by
> Mailtrack
> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>  06/01/23,
> 04:51:51 PM
>
> On Wed, May 31, 2023 at 10:45 AM Christoph Junghans 
> wrote:
>
>>
>>
>> On Tue, May 30, 2023 at 10:46 PM Kankana Bhattacharjee <
>> kankanabhattacharje...@gmail.com> wrote:
>>
>>> Ok sir.
>>>
>>> I have tried to perform boltzmann inversion after short (5 ps) atomistic
>>> MD run of propane. I am attaching the corresponding grompp.mdp file of the
>>> atomistic run, distributed bonded potential files, and boltzmann inverted
>>> bonded potential files. But, not understanding how these potential are
>>> helping in generating the itp file of CG propane.
>>>
>> Well once you have the inverted potentials you can use them in the CG
>> run, *.pot is the VOTCA format, which you have to convert to xvg (see
>> https://www.votca.org/csg/preparing.html#exporting-the-table)
>>
>> the table_a1 (a1 for Angle 1) and table_b1 (b1 for Bond 1) in the propane
>> tutorials were generated this way:
>> https://github.com/votca/votca/tree/master/csg-tutorials/propane/ibi
>>
>> And, the thing which I understood is that, boltzmann inversion is used
>>> for getting all atom inverted potential and force matching is used for
>>> getting non-bonded potentials.
>>>
>> For you can use iterative boltzmann inversion for the non-bonded
>> interactions.
>> (Force-matching works for bonded interactions as well, but VOTCA has
>> implemented that)
>>
>>
>>>
>>> CG propane itp  (topol.top) file is available in ibi/imc methods part of
>>> votca. Can it be supplied in performing CG-MD simulation using GROMACS ?
>>>
>> If you run the propane tutorial after a couple of steps you will have
>> some tabulated potential that you can use for CG-MD.
>>
>> Christoph
>>
>>>
>>>
>>>
>>>
>>> [image: Mailtrack]
>>> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>>>  Sender
>>> notified by
>>> Mailtrack
>>> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>>>  05/31/23,
>>> 10:12:10 AM
>>>
>>> On Wed, May 31, 2023 at 10:10 AM Christoph Junghans 
>>> wrote:
>>>
>>>>
>>>>
>>>> On Tue, May 30, 2023 at 10:33 PM Kankana Bhattacharjee <
>>>> kankanabhattacharje...@gmail.com> wrote:
>>>>
>>>>> Thank you sir. I would like to know, how can one get gromacs
>>>>> compatible itp file for a Coarse grained model using votca ?
>>>>>
>>>> It is all tabulated interaction, hence no itp files.
>>>>
>>>> And the interactions are determined by IBI, IMC or Force Matching,
>>>> whatever you prefer.
>>>>
>>>> Christoph
>>>>
>>>>>
>>>>>
>>>

Re: [votca] Regarding-Getting-itp-files:

[Christoph Junghans]

On Tue, May 30, 2023 at 10:46 PM Kankana Bhattacharjee <
kankanabhattacharje...@gmail.com> wrote:

> Ok sir.
>
> I have tried to perform boltzmann inversion after short (5 ps) atomistic
> MD run of propane. I am attaching the corresponding grompp.mdp file of the
> atomistic run, distributed bonded potential files, and boltzmann inverted
> bonded potential files. But, not understanding how these potential are
> helping in generating the itp file of CG propane.
>
Well once you have the inverted potentials you can use them in the CG run,
*.pot is the VOTCA format, which you have to convert to xvg (see
https://www.votca.org/csg/preparing.html#exporting-the-table)

the table_a1 (a1 for Angle 1) and table_b1 (b1 for Bond 1) in the propane
tutorials were generated this way:
https://github.com/votca/votca/tree/master/csg-tutorials/propane/ibi

And, the thing which I understood is that, boltzmann inversion is used for
> getting all atom inverted potential and force matching is used for getting
> non-bonded potentials.
>
For you can use iterative boltzmann inversion for the non-bonded
interactions.
(Force-matching works for bonded interactions as well, but VOTCA has
implemented that)


>
> CG propane itp  (topol.top) file is available in ibi/imc methods part of
> votca. Can it be supplied in performing CG-MD simulation using GROMACS ?
>
If you run the propane tutorial after a couple of steps you will have some
tabulated potential that you can use for CG-MD.

Christoph

>
>
>
>
> [image: Mailtrack]
> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>  Sender
> notified by
> Mailtrack
> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>  05/31/23,
> 10:12:10 AM
>
> On Wed, May 31, 2023 at 10:10 AM Christoph Junghans 
> wrote:
>
>>
>>
>> On Tue, May 30, 2023 at 10:33 PM Kankana Bhattacharjee <
>> kankanabhattacharje...@gmail.com> wrote:
>>
>>> Thank you sir. I would like to know, how can one get gromacs compatible
>>> itp file for a Coarse grained model using votca ?
>>>
>> It is all tabulated interaction, hence no itp files.
>>
>> And the interactions are determined by IBI, IMC or Force Matching,
>> whatever you prefer.
>>
>> Christoph
>>
>>>
>>>
>>>
>>> [image: Mailtrack]
>>> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>>>  Sender
>>> notified by
>>> Mailtrack
>>> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>>>  05/31/23,
>>> 10:02:22 AM
>>>
>>> On Wed, May 31, 2023 at 9:58 AM Christoph Junghans 
>>> wrote:
>>>
>>>>
>>>>
>>>> On Sun, May 28, 2023 at 10:13 PM Kankana Bhattacharjee <
>>>> kankanabhattacharje...@gmail.com> wrote:
>>>>
>>>>> Thanks a lot sir for your kind help.
>>>>>
>>>>> I have gone through the topol.top file of spce and propane model using
>>>>> ibi method. I have doubts, how did you define the mass of the beads,
>>>>> charge, bond and angle between beads in topol.top file of the CG model ?
>>>>>
>>>> For a center of mass mapping it is just the sum of the masses (and
>>>> charges), but of course you can do other mappings, too.
>>>>
>>>> In general making a coarse-grained model is more art than science.
>>>>
>>>> Christoph
>>>>
>>>>>
>>>>>
>>>>>
>>>>> [image: Mailtrack]
>>>>> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>>>>>  Sender
>>>>> notified by
>>>>> Mailtrack
>>>>> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>>>>>  05/29/23,
>>>>> 09:41:28 AM
>>>>>
>>>>> On Fri, May 26, 2023 at 9:15 PM Christoph Junghans 
>>>>> wrote:
>>>>>
>>>>>> On Thu, May 25, 2023 at 7:23 AM Kankana Bhattacharjee
>>>>>>  wrote:
>>>>>> >
>>>>>> > Dear Sir,
>>>>>> >
>>>>>> > I am learning votca. Now, I have done spce water model atomistic md
>>>>>> run. In the spce/atomistic foolder, grompp.mdp contains integrator as 
>>>>>> "sd"
>>>>>> . And, I used this settings for short MD r

Re: [votca] Regarding-Getting-itp-files:

[Christoph Junghans]

On Tue, May 30, 2023 at 10:33 PM Kankana Bhattacharjee <
kankanabhattacharje...@gmail.com> wrote:

> Thank you sir. I would like to know, how can one get gromacs compatible
> itp file for a Coarse grained model using votca ?
>
It is all tabulated interaction, hence no itp files.

And the interactions are determined by IBI, IMC or Force Matching, whatever
you prefer.

Christoph

>
>
>
> [image: Mailtrack]
> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>  Sender
> notified by
> Mailtrack
> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>  05/31/23,
> 10:02:22 AM
>
> On Wed, May 31, 2023 at 9:58 AM Christoph Junghans 
> wrote:
>
>>
>>
>> On Sun, May 28, 2023 at 10:13 PM Kankana Bhattacharjee <
>> kankanabhattacharje...@gmail.com> wrote:
>>
>>> Thanks a lot sir for your kind help.
>>>
>>> I have gone through the topol.top file of spce and propane model using
>>> ibi method. I have doubts, how did you define the mass of the beads,
>>> charge, bond and angle between beads in topol.top file of the CG model ?
>>>
>> For a center of mass mapping it is just the sum of the masses (and
>> charges), but of course you can do other mappings, too.
>>
>> In general making a coarse-grained model is more art than science.
>>
>> Christoph
>>
>>>
>>>
>>>
>>> [image: Mailtrack]
>>> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>>>  Sender
>>> notified by
>>> Mailtrack
>>> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>>>  05/29/23,
>>> 09:41:28 AM
>>>
>>> On Fri, May 26, 2023 at 9:15 PM Christoph Junghans 
>>> wrote:
>>>
>>>> On Thu, May 25, 2023 at 7:23 AM Kankana Bhattacharjee
>>>>  wrote:
>>>> >
>>>> > Dear Sir,
>>>> >
>>>> > I am learning votca. Now, I have done spce water model atomistic md
>>>> run. In the spce/atomistic foolder, grompp.mdp contains integrator as "sd"
>>>> . And, I used this settings for short MD run. Then, used csg_tool to
>>>> compute rdf of CG-CG beads and compared with CG-CG with ibi. Then, I dint
>>>> understand the "Running ibi" part of the spce model. It has been asked to
>>>> reduce the number of MD steps in grompp.mdp and adjust the equilibration
>>>> time in the settings.xml file. Exactly how to adjust this and why ? I have
>>>> skipped the "Running ibi" option.
>>>>
>>>> Well, the number of MD steps is in grompp.mdp, while the equilibration
>>>> time is in settings.xml. Longer run will give you smoother RDFs, and
>>>> the system usually needs some time to equilibrate from the initial
>>>> condition, so you don't want to pick that too short. In the tutorial
>>>> we ask folks to explore these options to get some feel for statistics.
>>>>
>>>> >
>>>> > Second;y, I did force matching part exactly. But, dint understand
>>>> exactly what is happening. Like, If I want to generate gromacs compatible
>>>> forcefield.itp for a coarse grained model and perform MD simulation using
>>>> gromacs. THen, how can I generate ttp file for a molecule.
>>>>
>>>>  Force matching return a tabulated force that can then be used to run
>>>> the coarse-grained simulation. Have a look at the topol.top of the
>>>> spce/ibi example.
>>>>
>>>> Christoph
>>>>
>>>> >
>>>> > Thanks & Regards
>>>> > Kankana Bhattacharjee
>>>> >
>>>> > --
>>>> > Join us on Slack: https://join.slack.com/t/votca/signup
>>>> > ---
>>>> > You received this message because you are subscribed to the Google
>>>> Groups "votca" group.
>>>> > To unsubscribe from this group and stop receiving emails from it,
>>>> send an email to votca+unsubscr...@googlegroups.com.
>>>> > To view this discussion on the web visit
>>>> https://groups.google.com/d/msgid/votca/c6eaf8c8-1963-4772-9800-dc9d839dd0bbn%40googlegroups.com
>>>> .
>>>>
>>>>
>>>>
>>>> --
>>>> Christoph Junghans
>>>> Web: http://www.compphys.de
>>>>
>>>> --
>>>> Join us on Slack: https://join.slack.com/t/votca/signup
>>>> ---
>>>> You received this message because you are subscribed to the Google
>>>> Groups "votca" group.
>>>> To unsubscribe from this group and stop receiving emails from it, send
>>>> an email to votca+unsubscr...@googlegroups.com.
>>>> To view this discussion on the web visit
>>>> https://groups.google.com/d/msgid/votca/CAHG27e73xWx4bDHzx2AAxA%2B8OaQC%2B_6ru%2B7iACRsRWZrDJOoqQ%40mail.gmail.com
>>>> .
>>>>
>>>
>>
>> --
>> Christoph Junghans
>> Web: http://www.compphys.de
>>
>

-- 
Christoph Junghans
Web: http://www.compphys.de

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Re: [votca] Generating-CG-itp-files:

[Christoph Junghans]

On Sun, May 28, 2023 at 11:56 PM Kankana Bhattacharjee
 wrote:
>
> Dear Sir,
>
> I am practicing the votca tutorial for propane molecule. I am trying to 
> generate .itp file of CG propane. For that I used the command line:
> csg_gmxtopol --topol.tpr --cg propane.xml --out cg.top, then obtained the top 
> file. But, there bond length and angle value between the beads is not 
> mentioned. How to get those bonded information of the beads so that, I can 
> run GROMACS simulation of the CG system ?

csg_gmxtopol only generates a template that can be used as a starting
point. In most cases you will have to edit it.
The bond and angle length you will have to estimate from the distributions.

>
> Also, I have gone through the topol.top file of the system using "ibi", "imc" 
> methods. But, there I dint understand how to use the function type for the 
> bonds, angles and how non-bonded settings is decided ?

In most cases people use tabulated interaction for everything.
Have a look at:
https://github.com/votca/votca/blob/master/csg-tutorials/propane/ibi/topol.top#L23
type =8 is tabulated.

Christoph

>
>
> Thanks & Regards
> Kankana Bhattacharjee
>
> --
> Join us on Slack: https://join.slack.com/t/votca/signup
> ---
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> "votca" group.
> To unsubscribe from this group and stop receiving emails from it, send an 
> email to votca+unsubscr...@googlegroups.com.
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> https://groups.google.com/d/msgid/votca/d54cdf42-089b-455e-892e-ce99327c7184n%40googlegroups.com.



-- 
Christoph Junghans
Web: http://www.compphys.de

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Re: [votca] Regarding-Getting-itp-files:

[Christoph Junghans]

On Sun, May 28, 2023 at 10:13 PM Kankana Bhattacharjee <
kankanabhattacharje...@gmail.com> wrote:

> Thanks a lot sir for your kind help.
>
> I have gone through the topol.top file of spce and propane model using ibi
> method. I have doubts, how did you define the mass of the beads, charge,
> bond and angle between beads in topol.top file of the CG model ?
>
For a center of mass mapping it is just the sum of the masses (and
charges), but of course you can do other mappings, too.

In general making a coarse-grained model is more art than science.

Christoph

>
>
>
> [image: Mailtrack]
> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>  Sender
> notified by
> Mailtrack
> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>  05/29/23,
> 09:41:28 AM
>
> On Fri, May 26, 2023 at 9:15 PM Christoph Junghans 
> wrote:
>
>> On Thu, May 25, 2023 at 7:23 AM Kankana Bhattacharjee
>>  wrote:
>> >
>> > Dear Sir,
>> >
>> > I am learning votca. Now, I have done spce water model atomistic md
>> run. In the spce/atomistic foolder, grompp.mdp contains integrator as "sd"
>> . And, I used this settings for short MD run. Then, used csg_tool to
>> compute rdf of CG-CG beads and compared with CG-CG with ibi. Then, I dint
>> understand the "Running ibi" part of the spce model. It has been asked to
>> reduce the number of MD steps in grompp.mdp and adjust the equilibration
>> time in the settings.xml file. Exactly how to adjust this and why ? I have
>> skipped the "Running ibi" option.
>>
>> Well, the number of MD steps is in grompp.mdp, while the equilibration
>> time is in settings.xml. Longer run will give you smoother RDFs, and
>> the system usually needs some time to equilibrate from the initial
>> condition, so you don't want to pick that too short. In the tutorial
>> we ask folks to explore these options to get some feel for statistics.
>>
>> >
>> > Second;y, I did force matching part exactly. But, dint understand
>> exactly what is happening. Like, If I want to generate gromacs compatible
>> forcefield.itp for a coarse grained model and perform MD simulation using
>> gromacs. THen, how can I generate ttp file for a molecule.
>>
>>  Force matching return a tabulated force that can then be used to run
>> the coarse-grained simulation. Have a look at the topol.top of the
>> spce/ibi example.
>>
>> Christoph
>>
>> >
>> > Thanks & Regards
>> > Kankana Bhattacharjee
>> >
>> > --
>> > Join us on Slack: https://join.slack.com/t/votca/signup
>> > ---
>> > You received this message because you are subscribed to the Google
>> Groups "votca" group.
>> > To unsubscribe from this group and stop receiving emails from it, send
>> an email to votca+unsubscr...@googlegroups.com.
>> > To view this discussion on the web visit
>> https://groups.google.com/d/msgid/votca/c6eaf8c8-1963-4772-9800-dc9d839dd0bbn%40googlegroups.com
>> .
>>
>>
>>
>> --
>> Christoph Junghans
>> Web: http://www.compphys.de
>>
>> --
>> Join us on Slack: https://join.slack.com/t/votca/signup
>> ---
>> You received this message because you are subscribed to the Google Groups
>> "votca" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to votca+unsubscr...@googlegroups.com.
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>> .
>>
>

-- 
Christoph Junghans
Web: http://www.compphys.de

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Re: [votca] Regarding-Getting-itp-files:

[Christoph Junghans]

On Thu, May 25, 2023 at 7:23 AM Kankana Bhattacharjee
 wrote:
>
> Dear Sir,
>
> I am learning votca. Now, I have done spce water model atomistic md run. In 
> the spce/atomistic foolder, grompp.mdp contains integrator as "sd" . And, I 
> used this settings for short MD run. Then, used csg_tool to compute rdf of 
> CG-CG beads and compared with CG-CG with ibi. Then, I dint understand the 
> "Running ibi" part of the spce model. It has been asked to reduce the number 
> of MD steps in grompp.mdp and adjust the equilibration time in the 
> settings.xml file. Exactly how to adjust this and why ? I have skipped the 
> "Running ibi" option.

Well, the number of MD steps is in grompp.mdp, while the equilibration
time is in settings.xml. Longer run will give you smoother RDFs, and
the system usually needs some time to equilibrate from the initial
condition, so you don't want to pick that too short. In the tutorial
we ask folks to explore these options to get some feel for statistics.

>
> Second;y, I did force matching part exactly. But, dint understand exactly 
> what is happening. Like, If I want to generate gromacs compatible 
> forcefield.itp for a coarse grained model and perform MD simulation using 
> gromacs. THen, how can I generate ttp file for a molecule.

 Force matching return a tabulated force that can then be used to run
the coarse-grained simulation. Have a look at the topol.top of the
spce/ibi example.

Christoph

>
> Thanks & Regards
> Kankana Bhattacharjee
>
> --
> Join us on Slack: https://join.slack.com/t/votca/signup
> ---
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-- 
Christoph Junghans
Web: http://www.compphys.de

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[votca] VOTCA in homebrew

[Christoph Junghans]

Hi users,

We are in the process of getting VOTCA into homebrew, but we are missing a
couple of GitHub stats!

So if you would like to see VOTCA in homebrew, please fork, star AND watch
the VOTCA repository on GitHub: https://github.com/votca/votca

Thanks,

Christoph

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Re: [votca] Error when do ibi for --first-frame 0' failed

[Christoph Junghans]

Annie,

is it working now?

Christoph

On Wednesday, May 10, 2023 at 1:45:42 PM UTC-6 wu.ann...@gmail.com wrote:

> get it, thanks for your explain, I will try it.
>
> On Thu, May 11, 2023 at 3:44 AM Christoph Junghans  
> wrote:
>
>>
>>
>> On Wed, May 10, 2023 at 1:40 PM Annie Wu  wrote:
>>
>>> If I change the volume to two time, how could I make sure the density is 
>>> correct? since I use nve to control the density and use pressure correction 
>>> to adjust the pressure. 
>>>
>> Sorry, I meant, take your original box and stack 8 of them together (2 in 
>> each dimension), so you have the same density.
>>
>> Christoph
>>  
>>
>>>
>>> On Thu, May 11, 2023 at 3:32 AM Christoph Junghans  
>>> wrote:
>>>
>>>>
>>>>
>>>> On Wed, May 10, 2023 at 1:00 PM Annie Wu  wrote:
>>>>
>>>>> [image: 截屏2023-05-11 02.58.44.png]
>>>>> I change the cutoff, but I think it's not very reasonable, I change it 
>>>>> to 0.35,it could run but with a new error, I have change table_begin for 
>>>>> 1-2 potential, but not very useful, is there any command I could change?
>>>>>
>>>> If changing the cutoff isn't reasonable, just make the simulation box 
>>>> bigger by a factor 2 in each direction.
>>>>
>>>> Christoph
>>>>  
>>>>
>>>>>
>>>>> On Thu, May 11, 2023 at 2:08 AM Christoph Junghans  
>>>>> wrote:
>>>>>
>>>>>>
>>>>>>
>>>>>> On Wed, May 10, 2023 at 12:01 PM Annie Wu  
>>>>>> wrote:
>>>>>>
>>>>>>> I change the data file with molecular id and added a topol.xml file, 
>>>>>>> updating the new attachment, really appreciate your reply, could you 
>>>>>>> have a 
>>>>>>> look at my files? Thanks  really alot.
>>>>>>>
>>>>>>> On Thu, May 11, 2023 at 1:40 AM Annie Wu  
>>>>>>> wrote:
>>>>>>>
>>>>>>>> Running critical command 'csg_stat --nt 6 --options 
>>>>>>>> /usr/local/share/votca/csg-tutorials/spce/ibi_lammps/try-ibi-lammps/settings.xml
>>>>>>>>  
>>>>>>>> --top topol.xml --trj traj.dump --begin 0 --first-frame 0'
>>>>>>>> begin to calculate distribution functions
>>>>>>>> # of bonded interactions: 0
>>>>>>>> # of non-bonded interactions: 3
>>>>>>>> I have 4000 beads in 800 molecules
>>>>>>>> Reading frame, timestep 1
>>>>>>>> an error occurred:
>>>>>>>> The max of interaction "CG1-CG1" bigger is than half the box.
>>>>>>>>
>>>>>>> This error means that the max of the CG1-CG1 interaction is larger 
>>>>>> than 1/2 box, which due to minimum image convention is not good, so 
>>>>>> suggest 
>>>>>> use a bigger box or a smaller cutoff.
>>>>>>
>>>>>>
>>>>>>>> Callstack:
>>>>>>>> /usr/local/share/votca/scripts/inverse/inverse.sh - linenumber 266
>>>>>>>> do_external - linenumber 177 in 
>>>>>>>> /usr/local/share/votca/scripts/inverse/functions_common.sh
>>>>>>>> /usr/local/share/votca/scripts/inverse/update_ibi.sh - 
>>>>>>>> linenumber 31
>>>>>>>> for_all - linenumber 22 (see 'csg_call --cat function 
>>>>>>>> for_all')
>>>>>>>> do_external - linenumber 19 (see 'csg_call 
>>>>>>>> --cat function do_external')
>>>>>>>> 
>>>>>>>> /usr/local/share/votca/scripts/inverse/calc_rdf_generic.sh - 
>>>>>>>> linenumber 84
>>>>>>>> critical - linenumber 4 (see 'csg_call 
>>>>>>>> --cat function critical')
>>>>>>>> die - linenumber 2 (see 'csg_call 
>>>>>>>> --cat function die')
>>>>>>>>
>>>>>>>> ##

Re: [votca] Regarding-Votca-Installation:

[Christoph Junghans]

On Fri, May 19, 2023, 04:48 Kankana Bhattacharjee <
kankanabhattacharje...@gmail.com> wrote:

> Dear Sir,
>
> I am going to install the VOTCA at "wsl" interface. While configuring.,
> i.e
> cmake -B builddir -S votca -DBUILD_XTP=ON
> -DCMAKE_INSTALL_PREFIX=${prefix=/mnt/c/Users/KANKANA/Downloads}
> Then, error is coming: -- Could NOT find MKL: Source the compilervars.sh
> or mklvars.sh scripts included with your installation of MKL. This script
> searches for the libraries in MKLROOT, LIBRARY_PATHS(Linux), and
> LIB(Windows) environment variables (missing: MKL_INCLUDE_DIR
> MKL_Core_LINK_LIBRARY MKL_Interface_LINK_LIBRARY
> MKL_ThreadLayer_LINK_LIBRARY)-- Could NOT find MKL: Source the
> compilervars.sh or mklvars.sh scripts included with your installation of
> MKL. This script searches for the libraries in MKLROOT,
> LIBRARY_PATHS(Linux), and LIB(Windows) environment variables (missing:
> MKL_INCLUDE_DIR MKL_Core_STATIC_LINK_LIBRARY
> MKL_Interface_STATIC_LINK_LIBRARY MKL_ThreadLayer_STATIC_LINK_LIBRARY)
>
This means MKL wasn't found, but that is just a warning and can be ignored.

The actual error is below where it says libxc wasn't found!

libxc is needed for the xtp part of Votca. However if you are not
interested in xtp, you can switch that off with the BUILD_XTP option.

Christoph

-- Found OpenMP_CXX: -fopenmp (Required is at least version "4.5")
> -- Found OpenMP: TRUE (Required is at least version "4.5")
>
> Not able to resolve this problem. Kindly help me with this.
>
> Thanks & Regards
> Kankana Bhattacharjee
> Ph. D. Scholar
> Department of Chemistry
> Ashoka University
> Sonipat, haryana
> -- HDF5: Using hdf5 compiler wrapper to determine CXX configuration
> -- Could NOT find LMP (missing: LMP_EXECUTABLE)
> -- Checking for module 'libxc'
> --   No package 'libxc' found
> CMake Error at
> /usr/share/cmake-3.16/Modules/FindPackageHandleStandardArgs.cmake:146
> (message):
>   Could NOT find Libxc (missing: Libxc_INCLUDE_DIR Libxc_LIBRARY)
> Call Stack (most recent call first):
>   /usr/share/cmake-3.16/Modules/FindPackageHandleStandardArgs.cmake:393
> (_FPHSA_FAILURE_MESSAGE)
>   CMakeModules/FindLibxc.cmake:37 (find_package_handle_standard_args)
>   xtp/CMakeLists.txt:7 (find_package)
>
>
> -- Configuring incomplete, errors occurred!
> See also
> "/mnt/c/Users/KANKANA/Downloads/builddir/CMakeFiles/CMakeOutput.log".
> See also
> "/mnt/c/Users/KANKANA/Downloads/builddir/CMakeFiles/CMakeError.log".
>
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> 
> .
>

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Re: [votca] Re: Problem converging to bonded potential (IBI)

[Christoph Junghans]

gt;>>>>> have only 1 bond type and 1 angle type. For this one I did try 
>>>>>>>>>>>>> optimizing
>>>>>>>>>>>>> separately to see if it would fix the problem and yet I reached 
>>>>>>>>>>>>> weird
>>>>>>>>>>>>> results. The second message had figures of a less coarsened 
>>>>>>>>>>>>> mapping (let's
>>>>>>>>>>>>> call it mapping B) in which I somewhat successfully converge to 
>>>>>>>>>>>>> potentials
>>>>>>>>>>>>> that yield more or less rightful distributions (apart from the 
>>>>>>>>>>>>> smoothness
>>>>>>>>>>>>> issue). I only brought up the results of the second mapping to 
>>>>>>>>>>>>> show that
>>>>>>>>>>>>> the same strategy "worked" for deriving bonded potentials via IBI 
>>>>>>>>>>>>> for
>>>>>>>>>>>>> another mapping. Sorry if I made it more confusing!
>>>>>>>>>>>>>
>>>>>>>>>>>>> Em quarta-feira, 26 de abril de 2023 às 08:29:58 UTC+2, Marvin
>>>>>>>>>>>>> Bernhardt escreveu:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> Hey Cecília,
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Oh ok, then it is probably not the interaction with the
>>>>>>>>>>>>>> non-bonded terms, that causes issues. But I believe something 
>>>>>>>>>>>>>> similar is
>>>>>>>>>>>>>> going on, that indeed has something to do with your system being 
>>>>>>>>>>>>>> a
>>>>>>>>>>>>>> solid/crystal:
>>>>>>>>>>>>>> IBI is a very good potential update scheme, when the degrees
>>>>>>>>>>>>>> of freedom are well separated. For molecules in liquids, angles 
>>>>>>>>>>>>>> and bonds
>>>>>>>>>>>>>> are usually well separated, i.e. changing the potential of one, 
>>>>>>>>>>>>>> does not
>>>>>>>>>>>>>> affect the dist of the other much. But multiple occurrences of 
>>>>>>>>>>>>>> equivalent
>>>>>>>>>>>>>> DoFs also need to be well separated for IBI to work well. In 
>>>>>>>>>>>>>> your case,
>>>>>>>>>>>>>> consider a single angle potential between three beads in the 
>>>>>>>>>>>>>> crystal is
>>>>>>>>>>>>>> changed, but all the others are kept constant. It will change the
>>>>>>>>>>>>>> distribution of that angle, but also have  effect on different 
>>>>>>>>>>>>>> angles. In
>>>>>>>>>>>>>> that case IBI is not providing a good potential update at each 
>>>>>>>>>>>>>> iteration.
>>>>>>>>>>>>>> What is happening in detail, I believe, is that the angle
>>>>>>>>>>>>>> potential of all angles is updated by IBI, but this leads to an
>>>>>>>>>>>>>> “overshoot”. The next iteration, IBI tries to compensate, but 
>>>>>>>>>>>>>> overshoots
>>>>>>>>>>>>>> again in the other direction. You can easily test if this is 
>>>>>>>>>>>>>> what is
>>>>>>>>>>>>>> happening, plotting even and uneven iterations separately, i.e. 
>>>>>>>>>>>>>> compare a
>>>>>>>>>>>>>> plot at iterations 10, 12, 14 with 11, 13, 15.
>>>>>>>>>>>>>> This has happened to me before with ring molecules, where the
>>>>>>>>>>>>>> situation is similar. A possible solution is to scale the 
>>>>>>>>>>>>>> update, by some
>>>>>>>>>>>>>> factor between 0 and 1 (I'd try 0.25).
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Also test this for the bond potential, I guess this is
>>>>>>>>>>>>>> happening there too, otherwise it should converge within ~20 
>>>>>>>>>>>>>> iterations.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Greetings,
>>>>>>>>>>>>>> Marvin
>>>>>>>>>>>>>> On Tuesday, 25 April 2023 at 10:25:59 UTC+2 Cecília Álvares
>>>>>>>>>>>>>> wrote:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Hey Marvin,
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Thanks a lot for the reply!
>>>>>>>>>>>>>>> I will have a look on the paper right now and do some
>>>>>>>>>>>>>>> thinking. In fact, I wanted to test the possibility of 
>>>>>>>>>>>>>>> optimizing the
>>>>>>>>>>>>>>> bonded potentials first and, after its optimization is done, 
>>>>>>>>>>>>>>> optimize the
>>>>>>>>>>>>>>> non-bonded. So basically there is no optimization of non-bonded 
>>>>>>>>>>>>>>> whatsover
>>>>>>>>>>>>>>> being done in my simulation. To build the target distributions, 
>>>>>>>>>>>>>>> I sampled
>>>>>>>>>>>>>>> an atomistic system in which the non-bonded forces were 
>>>>>>>>>>>>>>> artificially
>>>>>>>>>>>>>>> removed. After having a trajectory file of this AA system, I 
>>>>>>>>>>>>>>> built the
>>>>>>>>>>>>>>> corresponding target distributions to be used in VOTCA with 
>>>>>>>>>>>>>>> csg_stat. For
>>>>>>>>>>>>>>> what is worth it, the target distributions of angle and bond 
>>>>>>>>>>>>>>> don't seem at
>>>>>>>>>>>>>>> all weird relative to the "real ones", of when non-bonded 
>>>>>>>>>>>>>>> forces exist. And
>>>>>>>>>>>>>>> then, after having the target distributions, I set up the CG MD 
>>>>>>>>>>>>>>> simulations
>>>>>>>>>>>>>>> within the IBI to have only bonded potential also. So, besides 
>>>>>>>>>>>>>>> there being
>>>>>>>>>>>>>>> no non-bonded potential optimization, there is also no 
>>>>>>>>>>>>>>> non-bonded forces at
>>>>>>>>>>>>>>> all in my CG system. But I dont think this should be a problem, 
>>>>>>>>>>>>>>> right? It
>>>>>>>>>>>>>>> makes sense to entrust the CG bonded potentials to reproduce 
>>>>>>>>>>>>>>> the target
>>>>>>>>>>>>>>> distributions of the AA bonded potentials.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> What I did try also, and that is in allignment with your
>>>>>>>>>>>>>>> idea, was to set up two IBI runs: (1) one run to optimize
>>>>>>>>>>>>>>> *only* the potential for the bonds and keep the angle
>>>>>>>>>>>>>>> potential active (in this case the latter comes from a simple 
>>>>>>>>>>>>>>> BI) and (2)
>>>>>>>>>>>>>>> one run to optimize only the potential for the angles and keep 
>>>>>>>>>>>>>>> the bond
>>>>>>>>>>>>>>> potential active (in this case the latter comes from a simple 
>>>>>>>>>>>>>>> BI). In the
>>>>>>>>>>>>>>> case (1) it seems that I converge to a potential for bonds that 
>>>>>>>>>>>>>>> is quite
>>>>>>>>>>>>>>> able to reproduce the corresponding distribution, while in the 
>>>>>>>>>>>>>>> case (2) I
>>>>>>>>>>>>>>> converge more and more to potentials that give super weird 
>>>>>>>>>>>>>>> distributions
>>>>>>>>>>>>>>> (like with three weird peaks, as I showed in the figure above)
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Concerning the phase of the system: it is a solid system.
>>>>>>>>>>>>>>> More specifically, it is a coarsened grained version of ZIF8 in 
>>>>>>>>>>>>>>> which the
>>>>>>>>>>>>>>> whole repeating unit was assumed to be one bead. I know that 
>>>>>>>>>>>>>>> IBI has not at
>>>>>>>>>>>>>>> all been developed for solids and even further not for MOFs - 
>>>>>>>>>>>>>>> the goal is
>>>>>>>>>>>>>>> actually to derive potentials in the CG level using many 
>>>>>>>>>>>>>>> different
>>>>>>>>>>>>>>> strategies (IBI, FM, relative entropy) and evaluate the 
>>>>>>>>>>>>>>> results. In any
>>>>>>>>>>>>>>> case, I dont think that the fact that my system is a xtalline 
>>>>>>>>>>>>>>> solid could
>>>>>>>>>>>>>>> be the reason why my results are super weird (right?). It seems 
>>>>>>>>>>>>>>> like such a
>>>>>>>>>>>>>>> simple system when in the CG level.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> For what is worth it, I am also assessing different
>>>>>>>>>>>>>>> mappings. Following the same strategy of optimizing first 
>>>>>>>>>>>>>>> bonded-potential
>>>>>>>>>>>>>>> for a less coarsened mapping (2 beads), I am able to reach less 
>>>>>>>>>>>>>>> weird
>>>>>>>>>>>>>>> results. For example, you can find below the evolution of the 
>>>>>>>>>>>>>>> corresponding
>>>>>>>>>>>>>>> distributions as I perform more iterations for this system (it 
>>>>>>>>>>>>>>> has one bond
>>>>>>>>>>>>>>> type and two angle types). I think there is still a problem 
>>>>>>>>>>>>>>> since we can
>>>>>>>>>>>>>>> see some tendency of the distributions becoming non-smooth as I 
>>>>>>>>>>>>>>> do more
>>>>>>>>>>>>>>> iterations, but the results are definitely less weird.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> [image: picture.png]
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Em segunda-feira, 24 de abril de 2023 às 20:50:14 UTC+2,
>>>>>>>>>>>>>>> Marvin Bernhardt escreveu:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Hi Cecília,
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> I once encountered similar problems with bonded and
>>>>>>>>>>>>>>>> non-bonded interactions. See Fig. 9 of this paper
>>>>>>>>>>>>>>>> <https://pubs.acs.org/doi/10.1021/acs.jctc.2c00665>. In
>>>>>>>>>>>>>>>> short: The problem was that the potential update of the 
>>>>>>>>>>>>>>>> non-bonded has some
>>>>>>>>>>>>>>>> influence on the bonded distribution, and vice versa. But the 
>>>>>>>>>>>>>>>> potential
>>>>>>>>>>>>>>>> update is calculated as if they were independent.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> The fix in my case was to update the two interactions
>>>>>>>>>>>>>>>> alternately using `1 0` for
>>>>>>>>>>>>>>>> bonded and `0 1` for
>>>>>>>>>>>>>>>> non-bonded interactions. You could try something similar.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Otherwise, is your system liquid? Are there non-bonded
>>>>>>>>>>>>>>>> interactions that you are optimizing at the same time?
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Greetings,
>>>>>>>>>>>>>>>> Marvin
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> On Monday, 24 April 2023 at 16:56:42 UTC+2 Cecília Álvares
>>>>>>>>>>>>>>>> wrote:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Hey there,
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> I am currently trying to derive bonded potentials of a
>>>>>>>>>>>>>>>>> very simple CG system (containing only one bond type and one 
>>>>>>>>>>>>>>>>> angle type)
>>>>>>>>>>>>>>>>> using IBI. However, I have been failing miserably at doing 
>>>>>>>>>>>>>>>>> it: instead of
>>>>>>>>>>>>>>>>> reaching potentials that are better and better at reproducing 
>>>>>>>>>>>>>>>>> the target
>>>>>>>>>>>>>>>>> distributions for the bond and for the angle, I end up having 
>>>>>>>>>>>>>>>>> weider and
>>>>>>>>>>>>>>>>> weider distributions as I do the iterations. I am posting a 
>>>>>>>>>>>>>>>>> plot of the
>>>>>>>>>>>>>>>>> bond and angle distributions to give a glimpse on the 
>>>>>>>>>>>>>>>>> "weirdness". I have
>>>>>>>>>>>>>>>>> already tried:
>>>>>>>>>>>>>>>>> (1) providing very refined (small bin size and a lot of
>>>>>>>>>>>>>>>>> bins) target distributions of excelent quality (meaning not 
>>>>>>>>>>>>>>>>> noisy at all)
>>>>>>>>>>>>>>>>> for the bond and the angle. Similarly, I have also tried 
>>>>>>>>>>>>>>>>> using less refined
>>>>>>>>>>>>>>>>> target distributions (larger bin sizes and less amount of 
>>>>>>>>>>>>>>>>> bins).
>>>>>>>>>>>>>>>>> (2) varied a lot the setup in the settings.xml concerning
>>>>>>>>>>>>>>>>> bin sizes for the distributions to be built at each iteration 
>>>>>>>>>>>>>>>>> from the
>>>>>>>>>>>>>>>>> trajectory file. I have tried very small bin sizes as well as 
>>>>>>>>>>>>>>>>> large bin
>>>>>>>>>>>>>>>>> sizes.
>>>>>>>>>>>>>>>>> (3) increasing the size of my simulation box hoping that
>>>>>>>>>>>>>>>>> maybe it was all a problem of not having "enough statistics" 
>>>>>>>>>>>>>>>>> to build good
>>>>>>>>>>>>>>>>> distributions at each iteration within the trajectory file I 
>>>>>>>>>>>>>>>>> was collecting
>>>>>>>>>>>>>>>>> from my simulations.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> None of these things has worked and I think I ran out of
>>>>>>>>>>>>>>>>> ideas of what could possibly be the cause of the problem. 
>>>>>>>>>>>>>>>>> Does anyone have
>>>>>>>>>>>>>>>>> any insights?
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> I am also attaching my target distributions (this is the
>>>>>>>>>>>>>>>>> scenario in which I am feeding target distributions lot of 
>>>>>>>>>>>>>>>>> points and
>>>>>>>>>>>>>>>>> smaller bin size) and the settings.xml file for what is worth 
>>>>>>>>>>>>>>>>> it.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> [image: plots.png]
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> --
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Christoph Junghans
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Re: [votca] Error when do ibi for --first-frame 0' failed

[Christoph Junghans]

On Wed, May 10, 2023 at 9:02 AM Annie Wu  wrote:
>
> Hi votca,
>
> I work on a two-type CG system, trying to correct the non-bond potential, but 
> file at the first frame, I follow the example in spce:ibi_lammps, I believe I 
> have the same in.file and lammps part in setting.xml, but have no idea why 
> this error comes, any help will be appreciated, I attach the files below. 
> Thanks for your time.

What exactly is the error message?

>
> Best,
> Annie
>
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Re: [votca] Regarding parallel run of Force Matching

[Christoph Junghans]

On Sat, Apr 29, 2023 at 7:26 PM Sanjeet Singh  wrote:
>
> Hello Chirstoph,
>
> Thank you for your reply.
>
> For the sake of clarity, I have some question on the same line.
>
> I can run Force Matching only on 1 CPU
Yes! Unless you implement it ;-)

>
> That means if I want to perform FM on many interactions simultaneously, then 
> I need to have good amount of RAM in my system.
The memory usage is determined mainly by the block size, smaller block
size means less memory usage, but also less frames to average over and
hence rougher averages.

Christoph
>
> Please correct me if I am wrong.
>
> Thank you.
>
> Sanjeet
>
> On Friday, April 28, 2023 at 12:28:37 PM UTC-4 Christoph Junghans wrote:
>>
>> On Fri, Apr 28, 2023 at 6:26 AM Sanjeet Singh  wrote:
>> >
>> > Hello,
>> >
>> > I have installed VOTCA on cluster using Spack.
>> >
>> > And I would like to know that Can I run force matching in parallel 
>> > (multithreading)?
>> No, it is not implemented, yet.
>>
>> Christoph
>>
>> >
>> > Sorry, if the question is very trivial.
>> >
>> > Thank you.
>> >
>> > Sanjeet
>> >
>> > --
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>>
>>
>>
>> --
>> Christoph Junghans
>> Web: http://www.compphys.de
>
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Re: [votca] Regarding parallel run of Force Matching

[Christoph Junghans]

On Fri, Apr 28, 2023 at 6:26 AM Sanjeet Singh  wrote:
>
> Hello,
>
> I have installed VOTCA on cluster using Spack.
>
> And I would like to know that Can I run force matching in parallel 
> (multithreading)?
No, it is not implemented, yet.

Christoph

>
> Sorry, if the question is very trivial.
>
> Thank you.
>
> Sanjeet
>
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Re: [votca] Error when installing VOTCA on macOS Ventura 13.0.1

[Christoph Junghans]

On Tue, Apr 25, 2023 at 19:53 zongyun tsai  wrote:

> Dear Christoph,
> The attachment is the error message and lines after adding --verbose
> command.
>
Hmm, we test against gromacs-2023 all the time, but I don’t have enough
experience with macOS and homebrew to help here.

Two side notes:
1.) If you want to do coarse-graining you will need gromacs-2019 as
gromacs-2023 doesn’t support tabulated interactions anymore.
2.) you could try to have votca build its own gromacs version with
-DBUILD_OWN_GROMACS=On.

Christoph


> Sincerely,
> Glenn
>
> Christoph Junghans  於 2023年4月26日 週三 上午5:20寫道：
>
>>
>>
>> On Tue, Apr 25, 2023 at 00:47 zongyun tsai 
>> wrote:
>>
>>> Dear Christoph,
>>>
>>> My gromacs version is 2023.1, and was built by myself using homebrew.
>>>
>> Can you do a verbose build (add —verbose) and post the error message and
>> lines above again?
>>
>> Christoph
>>
>>
>>> Glenn
>>>
>>> Christoph Junghans 在 2023年4月24日 星期一晚上11:40:24 [UTC+8] 的信中寫道：
>>>
>>>> On Sun, Apr 23, 2023 at 11:26 PM zongyun tsai 
>>>> wrote:
>>>> >
>>>> > Dear Christoph
>>>> >
>>>> >
>>>> > (base) glenntsai@GlenndeAir ~ % cmake --build builddir --parallel 8
>>>> >
>>>> > [ 1%] Built target csg_inverse_manpage
>>>> >
>>>> > [ 2%] Built target csg_call_build
>>>> >
>>>> > [ 2%] Built target csg_call_manpage
>>>> >
>>>> > [ 2%] Built target csg_inverse_build
>>>> >
>>>> > [ 2%] Built target votca_tools_manpages
>>>> >
>>>> > [ 2%] Built target votca_csg_manpages
>>>> >
>>>> > Current git revision is b533e3901
>>>> >
>>>> > [ 2%] Built target gitversion
>>>> >
>>>> > [ 17%] Built target votca_tools
>>>> >
>>>> > [ 17%] Built target votca_property
>>>> >
>>>> > [ 17%] Built target unit_test_correlate
>>>> >
>>>> > [ 17%] Built target unit_test_cubicspline
>>>> >
>>>> > [ 19%] Built target unit_test_datacollection
>>>> >
>>>> > [ 19%] Built target unit_test_crosscorrelate
>>>> >
>>>> > [ 19%] Built target unit_test_calculator
>>>> >
>>>> > [ 20%] Built target unit_test_constants
>>>> >
>>>> > [ 20%] Built target unit_test_edge_base
>>>> >
>>>> > [ 22%] Built target unit_test_floatingpointcomparison
>>>> >
>>>> > [ 22%] Built target unit_test_filesystem
>>>> >
>>>> > [ 23%] Built target unit_test_elements
>>>> >
>>>> > [ 25%] Built target unit_test_graphalgorithm
>>>> >
>>>> > [ 26%] Built target unit_test_edgecontainer
>>>> >
>>>> > [ 26%] Built target unit_test_graph_base
>>>> >
>>>> > [ 26%] Built target unit_test_graphdistvisitor
>>>> >
>>>> > [ 26%] Built target unit_test_graph_df_visitor
>>>> >
>>>> > [ 26%] Built target unit_test_graphvisitor
>>>> >
>>>> > [ 28%] Built target unit_test_histogramnew
>>>> >
>>>> > [ 29%] Built target unit_test_graph_bf_visitor
>>>> >
>>>> > [ 31%] Built target unit_test_graphnode
>>>> >
>>>> > [ 31%] Built target unit_test_identity
>>>> >
>>>> > [ 31%] Built target unit_test_name
>>>> >
>>>> > [ 32%] Built target unit_test_objectfactory
>>>> >
>>>> > [ 34%] Built target unit_test_property
>>>> >
>>>> > [ 34%] Built target unit_test_linalg
>>>> >
>>>> > [ 34%] Built target unit_test_optionshandler
>>>> >
>>>> > [ 35%] Built target unit_test_reducededge
>>>> >
>>>> > [ 35%] Built target unit_test_reducedgraph
>>>> >
>>>> > [ 37%] Built target unit_test_structureparameters
>>>> >
>>>> > [ 37%] Built target unit_test_thread
>>>> >
>>>> > [ 38%] Built target unit_test_tokenizer
>>>> >
>>>> > [ 38%] Built target unit_test_table
>>>> >
>>>> > [ 38%] Built target unit_test_random
>>>> >
>&g

Re: [votca] Error when installing VOTCA on macOS Ventura 13.0.1

[Christoph Junghans]

On Tue, Apr 25, 2023 at 00:47 zongyun tsai  wrote:

> Dear Christoph,
>
> My gromacs version is 2023.1, and was built by myself using homebrew.
>
Can you do a verbose build (add —verbose) and post the error message and
lines above again?

Christoph


> Glenn
>
> Christoph Junghans 在 2023年4月24日 星期一晚上11:40:24 [UTC+8] 的信中寫道：
>
>> On Sun, Apr 23, 2023 at 11:26 PM zongyun tsai 
>> wrote:
>> >
>> > Dear Christoph
>> >
>> >
>> > (base) glenntsai@GlenndeAir ~ % cmake --build builddir --parallel 8
>> >
>> > [ 1%] Built target csg_inverse_manpage
>> >
>> > [ 2%] Built target csg_call_build
>> >
>> > [ 2%] Built target csg_call_manpage
>> >
>> > [ 2%] Built target csg_inverse_build
>> >
>> > [ 2%] Built target votca_tools_manpages
>> >
>> > [ 2%] Built target votca_csg_manpages
>> >
>> > Current git revision is b533e3901
>> >
>> > [ 2%] Built target gitversion
>> >
>> > [ 17%] Built target votca_tools
>> >
>> > [ 17%] Built target votca_property
>> >
>> > [ 17%] Built target unit_test_correlate
>> >
>> > [ 17%] Built target unit_test_cubicspline
>> >
>> > [ 19%] Built target unit_test_datacollection
>> >
>> > [ 19%] Built target unit_test_crosscorrelate
>> >
>> > [ 19%] Built target unit_test_calculator
>> >
>> > [ 20%] Built target unit_test_constants
>> >
>> > [ 20%] Built target unit_test_edge_base
>> >
>> > [ 22%] Built target unit_test_floatingpointcomparison
>> >
>> > [ 22%] Built target unit_test_filesystem
>> >
>> > [ 23%] Built target unit_test_elements
>> >
>> > [ 25%] Built target unit_test_graphalgorithm
>> >
>> > [ 26%] Built target unit_test_edgecontainer
>> >
>> > [ 26%] Built target unit_test_graph_base
>> >
>> > [ 26%] Built target unit_test_graphdistvisitor
>> >
>> > [ 26%] Built target unit_test_graph_df_visitor
>> >
>> > [ 26%] Built target unit_test_graphvisitor
>> >
>> > [ 28%] Built target unit_test_histogramnew
>> >
>> > [ 29%] Built target unit_test_graph_bf_visitor
>> >
>> > [ 31%] Built target unit_test_graphnode
>> >
>> > [ 31%] Built target unit_test_identity
>> >
>> > [ 31%] Built target unit_test_name
>> >
>> > [ 32%] Built target unit_test_objectfactory
>> >
>> > [ 34%] Built target unit_test_property
>> >
>> > [ 34%] Built target unit_test_linalg
>> >
>> > [ 34%] Built target unit_test_optionshandler
>> >
>> > [ 35%] Built target unit_test_reducededge
>> >
>> > [ 35%] Built target unit_test_reducedgraph
>> >
>> > [ 37%] Built target unit_test_structureparameters
>> >
>> > [ 37%] Built target unit_test_thread
>> >
>> > [ 38%] Built target unit_test_tokenizer
>> >
>> > [ 38%] Built target unit_test_table
>> >
>> > [ 38%] Built target unit_test_random
>> >
>> > [ 40%] Built target unit_test_akimaspline
>> >
>> > [ 41%] Built target unit_test_linspline
>> >
>> > [ 43%] Built target unit_test_unitconverter
>> >
>> > [ 43%] Built target votca_property_manpage
>> >
>> > [ 43%] Built target unit_test_NDimVector
>> >
>> > [ 43%] Built target unit_test_eigenio_matrixmarket
>> >
>> > [ 43%] Linking CXX shared library libvotca_csg.dylib
>> >
>> > Undefined symbols for architecture arm64:
>> >
>> > "read_first_frame(gmx_output_env_t const*, t_trxstatus**,
>> std::__1::__fs::filesystem::path const&, t_trxframe*, int)", referenced
>> from:
>> Hmm, this means something is wrong with the linking against gromacs?
>>
>> 0.) Do you need gromacs at all? - Otherwise switch it off.
>> 1.) What gromacs version are you using?
>> 2.) Did you build gromacs yourself?
>>
>> Christoph
>>
>> >
>> > votca::csg::GMXTrajectoryReader::FirstFrame(votca::csg::Topology&) in
>> gmxtrajectoryreader.cc.o
>> >
>> > "open_trx(std::__1::__fs::filesystem::path const&, char const*)",
>> referenced from:
>> >
>> > votca::csg::GMXTrajectoryWriter::Open(std::__1::basic_string> std::__1::char_traits, std::__1::allocator >, bool) in
>> gmxtrajectorywriter.cc.o
>> >
>>

Re: [votca] Error when installing VOTCA on macOS Ventura 13.0.1

[Christoph Junghans]

On Sun, Apr 23, 2023 at 11:26 PM zongyun tsai  wrote:
>
> Dear Christoph
>
>
> (base) glenntsai@GlenndeAir ~ % cmake --build builddir --parallel 8
>
> [  1%] Built target csg_inverse_manpage
>
> [  2%] Built target csg_call_build
>
> [  2%] Built target csg_call_manpage
>
> [  2%] Built target csg_inverse_build
>
> [  2%] Built target votca_tools_manpages
>
> [  2%] Built target votca_csg_manpages
>
> Current git revision is b533e3901
>
> [  2%] Built target gitversion
>
> [ 17%] Built target votca_tools
>
> [ 17%] Built target votca_property
>
> [ 17%] Built target unit_test_correlate
>
> [ 17%] Built target unit_test_cubicspline
>
> [ 19%] Built target unit_test_datacollection
>
> [ 19%] Built target unit_test_crosscorrelate
>
> [ 19%] Built target unit_test_calculator
>
> [ 20%] Built target unit_test_constants
>
> [ 20%] Built target unit_test_edge_base
>
> [ 22%] Built target unit_test_floatingpointcomparison
>
> [ 22%] Built target unit_test_filesystem
>
> [ 23%] Built target unit_test_elements
>
> [ 25%] Built target unit_test_graphalgorithm
>
> [ 26%] Built target unit_test_edgecontainer
>
> [ 26%] Built target unit_test_graph_base
>
> [ 26%] Built target unit_test_graphdistvisitor
>
> [ 26%] Built target unit_test_graph_df_visitor
>
> [ 26%] Built target unit_test_graphvisitor
>
> [ 28%] Built target unit_test_histogramnew
>
> [ 29%] Built target unit_test_graph_bf_visitor
>
> [ 31%] Built target unit_test_graphnode
>
> [ 31%] Built target unit_test_identity
>
> [ 31%] Built target unit_test_name
>
> [ 32%] Built target unit_test_objectfactory
>
> [ 34%] Built target unit_test_property
>
> [ 34%] Built target unit_test_linalg
>
> [ 34%] Built target unit_test_optionshandler
>
> [ 35%] Built target unit_test_reducededge
>
> [ 35%] Built target unit_test_reducedgraph
>
> [ 37%] Built target unit_test_structureparameters
>
> [ 37%] Built target unit_test_thread
>
> [ 38%] Built target unit_test_tokenizer
>
> [ 38%] Built target unit_test_table
>
> [ 38%] Built target unit_test_random
>
> [ 40%] Built target unit_test_akimaspline
>
> [ 41%] Built target unit_test_linspline
>
> [ 43%] Built target unit_test_unitconverter
>
> [ 43%] Built target votca_property_manpage
>
> [ 43%] Built target unit_test_NDimVector
>
> [ 43%] Built target unit_test_eigenio_matrixmarket
>
> [ 43%] Linking CXX shared library libvotca_csg.dylib
>
> Undefined symbols for architecture arm64:
>
>   "read_first_frame(gmx_output_env_t const*, t_trxstatus**, 
> std::__1::__fs::filesystem::path const&, t_trxframe*, int)", referenced from:
Hmm, this means something is wrong with the linking against gromacs?

0.) Do you need gromacs at all? - Otherwise switch it off.
1.) What gromacs version are you using?
2.) Did you build gromacs yourself?

Christoph

>
>   votca::csg::GMXTrajectoryReader::FirstFrame(votca::csg::Topology&) in 
> gmxtrajectoryreader.cc.o
>
>   "open_trx(std::__1::__fs::filesystem::path const&, char const*)", 
> referenced from:
>
>   votca::csg::GMXTrajectoryWriter::Open(std::__1::basic_string std::__1::char_traits, std::__1::allocator >, bool) in 
> gmxtrajectorywriter.cc.o
>
>   "read_tpx(std::__1::__fs::filesystem::path const&, t_inputrec*, float (*) 
> [3], int*, float (*) [3], float (*) [3], gmx_mtop_t*)", referenced from:
>
>   
> votca::csg::GMXTopologyReader::ReadTopology(std::__1::basic_string std::__1::char_traits, std::__1::allocator >, 
> votca::csg::Topology&) in gmxtopologyreader.cc.o
>
> ld: symbol(s) not found for architecture arm64
>
> clang: error: linker command failed with exit code 1 (use -v to see 
> invocation)
>
> make[2]: *** [csg/src/libcsg/libvotca_csg.2024.dylib] Error 1
>
> make[1]: *** [csg/src/libcsg/CMakeFiles/votca_csg.dir/all] Error 2
>
> make: *** [all] Error 2
>
>
>
> Glenn
>
>
> Christoph Junghans 在 2023年4月24日 星期一上午11:51:51 [UTC+8] 的信中寫道：
>>
>> On Sun, Apr 23, 2023 at 19:38 zongyun tsai  wrote:
>>>
>>> Hello,
>>> I encountered an Error message while when running the following command:
>>> cmake --build builddirThe error shown in the terminal states that
>>>
>>> clang: error: linker command failed with exit code 1 (use -v to see 
>>> invocation)
>>
>> can you post the lines above this error?
>>
>> Christoph
>>>
>>> make[2]: *** [csg/src/libcsg/libvotca_csg.2024.dylib] Error 1
>>>
>>> make[1]: *** [csg/src/libcsg/CMakeFiles/votca_csg.dir/all] Error 2
&

Re: [votca] Error when installing VOTCA on macOS Ventura 13.0.1

[Christoph Junghans]

On Sun, Apr 23, 2023 at 19:38 zongyun tsai  wrote:

> Hello,
> I encountered an Error message while when running the following command:
> cmake --build builddirThe error shown in the terminal states that
>
> clang: *error: **linker command failed with exit code 1 (use -v to see
> invocation)*
>
can you post the lines above this error?

Christoph

> make[2]: *** [csg/src/libcsg/libvotca_csg.2024.dylib] Error 1
>
> make[1]: *** [csg/src/libcsg/CMakeFiles/votca_csg.dir/all] Error 2
>
> make: *** [all] Error 2
> Can you please suggest some ways to correct this error?
> Thank you,Glenn
>
>
>
>
> --
> Join us on Slack: https://join.slack.com/t/votca/signup
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> .
>
-- 
Christoph Junghans
Web: http://www.compphys.de

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Re: [votca] Some question about only using single tabular potential in gromacs

[Christoph Junghans]

On Sun, Apr 9, 2023 at 9:01 AM Ran Zhao  wrote:
>
> Hello, I am preparing to simulate the polymer in a water solution using the 
> Martini force field.
> In the simulation model, I want to set a specific tabular potential between 
> water beads. And other beads still follow the martini force field.
>
> In gromacs, when one wants to use tabular potential, some lines should be 
> added in .mdp file:
> vdwtype= User
> rvdw  = 1.0
> energygrps   = POL (the name of type of water bead)
> energygrp_table   = POL POL
> the mdrun command will read the table_POL_POL.xvg
> But, I want mdrun to read the force field of other beads from the martini 
> .itp file.
> Is it possible for me to do this in gromacs?
I think this is more a question for the gromacs mailing list, but as
far as I know you cannot mix tabulated with non-tabulated
interactions.
You can still make that work as Gromacs will read a standard LJ 6-12
table (table.xvg) for all groups that aren't covered by the pairs in
energygrp_table though.

Christoph

> Looking forward to and thank you for your answer
>
> Sincerely yours
> Ran
>
> --
> Join us on Slack: https://join.slack.com/t/votca/signup
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-- 
Christoph Junghans
Web: http://www.compphys.de

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Re: [votca] Problem in reading mol id from .dump LAMMPS file

[Christoph Junghans]

On Mon, Feb 27, 2023 at 8:23 PM Sanjeet Singh  wrote:

> Dear Christoph,
>
> Thank you for your prompt response.
>
> Sorry, I didn't convey my points clearly. I want to say that atom with id
> 766 is a single atom cation. In CG representation, it is a bead consisting
> of only one atom. While atom with id 780 is an atom belonging to an anion
> consisting of 15 atoms. Below I have attached the details from the LAMMPS
> trajectory file.
>
> idmol type   q  x  y
>  zfx   fy  fz
>
> 766  12   71 1.29656  21.7926
> 13.5263 -0.34422 0.0733004 -0.408895
>
> 780  13  5-0.118  15.8523  12.1644
> 1.58685-0.908541 2.12485  -4.0017
>
> So, atoms with id 766 and 780 are not part of a single bead. In fact, they
> are not part of the same molecule. Therefore, there is no point in checking
> the condition "coarse-grained bead is bigger than half the box".
>
> Actually, my system consists of 10 polymer chains and 7 ion pairs. So, I
> have three types of molecules in my system: first polymer, second anion,
> and third cation. And, in the LAMMPS data file the atoms are listed such
> that first, it gives the coordinates of the atoms of the 10 polymer chains,
> followed by the coordinates of the first anion and cation, then the
> coordinates of the second anion and cation, and so on.
>
> But, csg_stat is reading the trajectory in such a way that the LAMMPS data
> file first lists the coordinates of the 10 polymer chains, followed by the
> coordinates of the 7 anions in my system, and then the 7 cations, which is
> not the correct order.
>
Sorry isn't that the order how you list it in your topology.xml? You can
run "csg_dump --top topology.xml" to see the order VOTCA is expecting.
The actual order in the dump file doesn't matter, VOTCA reads the atom id
and then stores it in the right spot, you can test that by doing a dummy
mapping (csg_map --no-map --trj file.dump --out file.xyz)

Christoph


>
> I have also verified this using the csg_dump command. I have also
> rechecked my mapping and topology files, I didn't find any mistakes in
> these files.
>
> Can you please suggest to me how to correct this? Maybe a possible
> workaround for this?
>
> Thank you.
>
> Sanjeet
>
> On Mon, Feb 27, 2023 at 4:30 PM Christoph Junghans 
> wrote:
>
>>
>>
>> On Sun, Feb 26, 2023 at 11:38 Sanjeet Singh  wrote:
>>
>>> Hello Everyone,
>>>
>>> I am trying to generate RDF for a Homopolymer electrolyte system using
>>> csg_stat command as below:
>>>
>>> csg_stat --top topology.xml --trj Trajectory2.dump --cg
>>> "PL.xml;SI.xml;L.xml" --options NONBON-RDF.xml
>>>
>>> But, I am getting the below error:
>>>
>>> Reading frame, timestep 0
>>> 0.129656
>>>  2.17926
>>>  1.35263  1.58523
>>>  1.21644
>>> 0.158685
>>> an error occurred:
>>> coarse-grained bead is bigger than half the box
>>>  (atoms CT1 (id 766), FT15 (id 780), molecule 12)
>>>
>>> From the above message, it can be seen that the error occurred at
>>> timestep 0. So, I tried to verify the error. The coordinates of the atoms
>>> with id 766 and id 780 are read correctly from the trajectory file. But,
>>> atom CT1 and FT15 belong to molecule 13, and not 12. CT1 should be actually
>>> LI1 as per my topology.
>>>
>> 12 vs 13 is C numbering that starts with 0, so 0, 1, 2.
>>
>> How big is your box and is any of the 3 distances in x,y or z bigger than
>> half of that?
>>
>> Usually this error hints at an error in the mapping, but if you are 100%
>> sure, that is right but increase the box size.
>>
>> Christoph
>>
>>
>>> Actually, my system consists of 10 polymer chains and 7 ion pairs. So, I
>>> have three types of molecules in my system: first polymer, second anion,
>>> and third cation. And, in the LAMMPS data file the atoms are listed such
>>> that first it gives the coordinates of the atoms of the 10 polymer chains,
>>> followed by the coordinates of the first anion and cation, then the
>>> coordinates of the second anion and cation, and so on.
>>>
>>> But, csg_stat is reading the trajectory in such a way that the LAMMPS
>>> data file first lists the coordinates of the 10 polymer chains, followed by
>>> the coordinates of the 7 anions in my system, and then the 7 cations, which
>>> is not the correct ord

Re: [votca] Problem in reading mol id from .dump LAMMPS file

[Christoph Junghans]

On Sun, Feb 26, 2023 at 11:38 Sanjeet Singh  wrote:

> Hello Everyone,
>
> I am trying to generate RDF for a Homopolymer electrolyte system using
> csg_stat command as below:
>
> csg_stat --top topology.xml --trj Trajectory2.dump --cg
> "PL.xml;SI.xml;L.xml" --options NONBON-RDF.xml
>
> But, I am getting the below error:
>
> Reading frame, timestep 0
> 0.129656
>  2.17926
>  1.35263  1.58523
>  1.21644
> 0.158685
> an error occurred:
> coarse-grained bead is bigger than half the box
>  (atoms CT1 (id 766), FT15 (id 780), molecule 12)
>
> From the above message, it can be seen that the error occurred at timestep
> 0. So, I tried to verify the error. The coordinates of the atoms with id
> 766 and id 780 are read correctly from the trajectory file. But, atom CT1
> and FT15 belong to molecule 13, and not 12. CT1 should be actually LI1 as
> per my topology.
>
12 vs 13 is C numbering that starts with 0, so 0, 1, 2.

How big is your box and is any of the 3 distances in x,y or z bigger than
half of that?

Usually this error hints at an error in the mapping, but if you are 100%
sure, that is right but increase the box size.

Christoph


> Actually, my system consists of 10 polymer chains and 7 ion pairs. So, I
> have three types of molecules in my system: first polymer, second anion,
> and third cation. And, in the LAMMPS data file the atoms are listed such
> that first it gives the coordinates of the atoms of the 10 polymer chains,
> followed by the coordinates of the first anion and cation, then the
> coordinates of the second anion and cation, and so on.
>
> But, csg_stat is reading the trajectory in such a way that the LAMMPS data
> file first lists the coordinates of the 10 polymer chains, followed by the
> coordinates of the 7 anions in my system, and then the 7 cations, which is
> not the correct order.
>
> I have also verified this using csg_dump command.
>
> Can you please suggest to me how to correct this? Maybe a possible
> workaround for this?
>
> Please find attached my topology, and mapping file.
>
> Thank you.
>
> Sanjeet
>
>
>
>
>
>
>
>
>
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>
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Re: [votca] Regarding CG approach to be used for deriving the potential for Homopolymer Electrolytes system

[Christoph Junghans]

On Wed, Feb 22, 2023 at 7:03 AM Sanjeet Singh  wrote:
>
> Dear Christoph,
>
> Thank you for your reply.
>
> I have another query though. In the VOTCA tutorial for liquid hexane with FM 
> for non-bonded interactions only, it is mentioned that we have to exclude all 
> the intramolecular interactions also in addition to the all bonded 
> interaction. I am not getting why we need to exclude the intramolecular 
> nonbonded interaction also? Because, I think these interactions needs to be 
> accounted in the nonbonded interactions part.

The coarse-grained topology has #excl of 3
(https://github.com/votca/votca/blob/master/csg-tutorials/hexane/ibi_nonbonded/topol.top#L13)
hence the A and B beads within a CG molecule don't interaction via
non-bonded interaction and so are fully covered by the bonded
interaction, which then means you need to exclude them for the
non-bonded interaction calculation.
I think this should be explained in more detail here:
http://dx.doi.org/10.1002/mats.201100011

However the setup of #excl of 3 is a gromacs inspired, and you could
certainly build a cg model where the A and B beads inside a molecule
also interact via non-bonded interactions. This is more common when
using lammps though.

Christoph
>
> Can you please clarify me on this.
>
> Thank you.
>
> Sanjeet
>
> On Monday, February 20, 2023 at 9:36:33 AM UTC-5 Christoph Junghans wrote:
>>
>> On Sat, Feb 18, 2023 at 8:26 PM Sanjeet Singh  wrote:
>> >
>> > Hello Everyone,
>> >
>> > I would like to derive the CG potential for a Homopolymer Electrolyte 
>> > system. But, I am confused that which approach among IBI, FM or REM would 
>> > be better.
>> >
>> > I know that IBI is not good for dilute system, considering the number of 
>> > ion pairs present in the system compared to the polymer.
>> You are right, getting enough statistics for IBI in dilute systems can
>> be cumbersome. I would try FM for the ions.
>> And you can always combine it with an IBI potential for the polymer.
>>
>> Christoph
>>
>> >
>> > Any suggestion would be of great help.
>> >
>> > Thank you.
>> >
>> > Sanjeet
>> >
>> > --
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>>
>>
>>
>> --
>> Christoph Junghans
>> Web: http://www.compphys.de
>
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Re: [votca] Regarding CG approach to be used for deriving the potential for Homopolymer Electrolytes system

[Christoph Junghans]

On Sat, Feb 18, 2023 at 8:26 PM Sanjeet Singh  wrote:
>
> Hello Everyone,
>
> I would like to derive the CG potential for a Homopolymer Electrolyte system. 
> But, I am confused that which approach among IBI, FM or REM would be better.
>
> I know that IBI is not good for dilute system, considering the number of ion 
> pairs present in the system compared to the polymer.
You are right, getting enough statistics for IBI in dilute systems can
be cumbersome. I would try FM for the ions.
And you can always combine it with an IBI potential for the polymer.

Christoph

>
> Any suggestion would be of great help.
>
> Thank you.
>
> Sanjeet
>
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Re: Re: [votca] Re: An issue in generating topology from Gmx file

[Christoph Junghans]

That option will use a built-in version of gromacs and not the one you
had compiled yourself, but whatever works for you.
My guess is, you didn't build gromacs with -DGMX_INSTALL_LEGACY_API=ON
and hence VOTCA didn't pick it up.

Christoph

On Thu, Feb 16, 2023 at 9:32 AM 张恒悦  wrote:
>
> Hi Christoph,
>
> I guess that I figure out what you mean. I compiled votca again with the flag 
> -DBUILD_OWN_GROMACS=ON, and this time this command worked well.
> Feeling sry for my poor English! Thx a lot!
>
> Best regards,
> Hengyue Zhang
>
> 发件人：Christoph Junghans 
> 发送日期：2023-02-16 00:47:16
> 收件人：votca@googlegroups.com
> 主题：Re: [votca] Re: An issue in generating topology from Gmx file
>
> Let me clarify: when you build votca did it pick up your gromacs install? 
> (Check the cmake output.)
>
> Christoph
>
> On Wed, Feb 15, 2023 at 03:17 张恒悦  wrote:
>>
>> No, gromacs was compiled independently. I compiled gromacs first then votca.
>>
>>
>>  Replied Message 
>> From Christoph Junghans Date 02/15/2023 07:31 To 
>> votca@googlegroups.com Cc Subject Re: [votca] Re: An issue in generating 
>> topology from Gmx file
>> Quick question, is VOTCA compiled the gromacs support?
>>
>> Christoph
>>
>> On Tue, Feb 14, 2023 at 10:51 Victor Zh  wrote:
>> I am the one who prompted this issue yesterday. I'd like to provide the 
>> files to describe my issue better.
>> Thanks a lot, the developers!
>>
>> Hengyue Zhang
>>
>> 在2023年2月13日星期一 UTC+8 23:16:13<张恒悦> 写道：
>> Hi,
>> Sorry for disturbing you! I am trying to generate topology file with the 
>> program xtp_map. After I inputted the following command, it replies
>> $ xtp_map -t MD_FILES/npt.tpr -c MD_FILES/PEN0.gro -s mapping.xml -f 
>> state.hdf5
>> ==
>>    VOTCA (http://www.votca.org)   
>> ==
>>
>> please submit bugs to https://github.com/votca/votca/issues
>>
>> xtp_map, version 2024-dev gitid: e0a61dbe1 (compiled Feb 13 2023, 20:13:21)
>>
>> an error occurred:
>> Error 'tpr' file format of file 'MD_FILES/npt.tpr' cannot be read or written
>> I am wondering why it replies as this. From the tutorials I got the 
>> knowledge and input the command as the tutorials guided me. I checked the 
>> authority of the tpr file, and it looks that there were no problems. So I am 
>> wondering how to fix this problem.
>> What's more, I assume that tpr file is not necessary in this command. I 
>> think that tpr file is the sum of top, gro and mdp file. And I have provided 
>> the gro file after -c flag, so I guess that only a top file is needed and 
>> what shows in mdp file is not necessary...?
>> I sincerely hope that you can reply when you are not busy. With my greatest 
>> gratitude!
>>
>> Best regards,
>> Hengyue Zhang
>>
>> --
>> Join us on Slack: https://join.slack.com/t/votca/signup
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>> --
>> Christoph Junghans
>> Web: http://www.compphys.de
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>>
>>
>>
>> 张恒悦 Hengyue Zhang
>> 天津大学化工学院
>> 地址：天津市津南区海河教育园区雅观路135号天津大学（300354）
>> School of Chemical Engineering and Technology, Tianjin University
>> Add: No. 135 Yaguan Rd., Tianjin, P. R. China (300354)
>> 南开大学化学学院
>> 地址：天津市南开区学府街道卫津路94号南开大学（300071）
>> College of Chemistry, Nankai University
>> Add: No. 94 Weijin Rd., Tianjin, P. R. China (300071)
>> Email: pds...@tju.edu.cn / pds...@mail.nankai.edu.cn
>> Tel: +86 137 2187 2381
>>
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