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
#
#
#
##################################################################################################################
Terminated
Kindly help me with this.
Thanks & Regards
kankana Bhattacharjee
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06/05/23,
10:44:51 AM
On Sat, Jun 3, 2023 at 8:42 PM Christoph Junghans <[email protected]>
wrote:
>
>
> On Sat, Jun 3, 2023 at 9:00 AM Kankana Bhattacharjee <
> [email protected]> 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 <[email protected]> wrote:
>>
>>>
>>>
>>> On Sat, Jun 3, 2023 at 3:16 AM Kankana Bhattacharjee <
>>> [email protected]> 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 <
>>>> [email protected]> 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&utm_medium=signature&utm_campaign=signaturevirality11&;>
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>>>>> 06/03/23,
>>>>> 09:45:05 AM
>>>>>
>>>>> On Sat, Jun 3, 2023 at 9:42 AM Christoph Junghans <[email protected]>
>>>>> wrote:
>>>>>
>>>>>>
>>>>>>
>>>>>> On Fri, Jun 2, 2023 at 21:00 Kankana Bhattacharjee <
>>>>>> [email protected]> 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&utm_medium=signature&utm_campaign=signaturevirality11&;>
>>>>>>> Sender
>>>>>>> notified by
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>>>>>>> 06/03/23,
>>>>>>> 08:29:51 AM
>>>>>>>
>>>>>>> On Sat, Jun 3, 2023 at 4:15 AM Christoph Junghans <
>>>>>>> [email protected]> wrote:
>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On Fri, Jun 2, 2023 at 12:34 PM Kankana Bhattacharjee <
>>>>>>>> [email protected]> 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&utm_medium=signature&utm_campaign=signaturevirality11&;>
>>>>>>>>> Sender
>>>>>>>>> notified by
>>>>>>>>> Mailtrack
>>>>>>>>> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&;>
>>>>>>>>> 06/03/23,
>>>>>>>>> 12:00:35 AM
>>>>>>>>>
>>>>>>>>> On Fri, Jun 2, 2023 at 9:13 PM Christoph Junghans <
>>>>>>>>> [email protected]> wrote:
>>>>>>>>>
>>>>>>>>>> Forgot to CC the mailing list, so here is the answer for others.
>>>>>>>>>>
>>>>>>>>>> ---------- Forwarded message ---------
>>>>>>>>>> From: Christoph Junghans <[email protected]>
>>>>>>>>>> Date: Fri, Jun 2, 2023 at 8:22 AM
>>>>>>>>>> Subject: Re: [votca] Regarding-Getting-itp-files:
>>>>>>>>>> To: Kankana Bhattacharjee <[email protected]>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On Fri, Jun 2, 2023 at 8:06 AM Kankana Bhattacharjee <
>>>>>>>>>> [email protected]> 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&utm_medium=signature&utm_campaign=signaturevirality11&;>
>>>>>>>>>>> Sender
>>>>>>>>>>> notified by
>>>>>>>>>>> Mailtrack
>>>>>>>>>>> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&;>
>>>>>>>>>>> 06/02/23,
>>>>>>>>>>> 07:34:36 PM
>>>>>>>>>>>
>>>>>>>>>>> On Fri, Jun 2, 2023 at 7:27 PM Christoph Junghans <
>>>>>>>>>>> [email protected]> wrote:
>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> On Fri, Jun 2, 2023 at 7:44 AM Kankana Bhattacharjee <
>>>>>>>>>>>> [email protected]> 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 <[email protected]>
>>>>>>>>>>>>> Date: Fri, Jun 2, 2023 at 7:10 PM
>>>>>>>>>>>>> Subject: Re: [votca] Regarding-Getting-itp-files:
>>>>>>>>>>>>> To: Kankana Bhattacharjee <[email protected]>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Fri, Jun 2, 2023 at 3:40 AM Kankana Bhattacharjee <
>>>>>>>>>>>>> [email protected]> 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&utm_medium=signature&utm_campaign=signaturevirality11&;>
>>>>>>>>>>>>>> Sender
>>>>>>>>>>>>>> notified by
>>>>>>>>>>>>>> Mailtrack
>>>>>>>>>>>>>> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&;>
>>>>>>>>>>>>>> 06/02/23,
>>>>>>>>>>>>>> 03:05:36 PM
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> On Fri, Jun 2, 2023 at 11:06 AM Kankana Bhattacharjee <
>>>>>>>>>>>>>> [email protected]> 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&utm_medium=signature&utm_campaign=signaturevirality11&;>
>>>>>>>>>>>>>>> Sender
>>>>>>>>>>>>>>> notified by
>>>>>>>>>>>>>>> Mailtrack
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>>>>>>>>>>>>>>> 06/02/23,
>>>>>>>>>>>>>>> 11:03:20 AM
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> On Fri, Jun 2, 2023 at 9:49 AM Kankana Bhattacharjee <
>>>>>>>>>>>>>>> [email protected]> wrote:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Dear Sir,
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> I used this command line for bonded distribution:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> csg_boltzmann --top topol.tpr --trj traj.trr --cg
>>>>>>>>>>>>>>>> propane.xml < boltzmann_cmds
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> After that, got average bond length and angle distribution.
>>>>>>>>>>>>>>>> And, bond section is already present in my propane.xml file.
>>>>>>>>>>>>>>>> But, still
>>>>>>>>>>>>>>>> dint get any plottable bond1.dist.ib and bond2.dist.ib files.
>>>>>>>>>>>>>>>> I am attaching the files here.
>>>>>>>>>>>>>>>> Please kindly help me
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Thanks & Regards
>>>>>>>>>>>>>>>> Kankana Bhattacharjee
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> [image: Mailtrack]
>>>>>>>>>>>>>>>> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&;>
>>>>>>>>>>>>>>>> Sender
>>>>>>>>>>>>>>>> notified by
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>>>>>>>>>>>>>>>> 06/02/23,
>>>>>>>>>>>>>>>> 09:37:49 AM
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> On Fri, Jun 2, 2023 at 7:26 AM Christoph Junghans <
>>>>>>>>>>>>>>>> [email protected]> wrote:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> On Thu, Jun 1, 2023 at 5:22 AM Kankana Bhattacharjee <
>>>>>>>>>>>>>>>>> [email protected]> 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&utm_medium=signature&utm_campaign=signaturevirality11&;>
>>>>>>>>>>>>>>>>>> Sender
>>>>>>>>>>>>>>>>>> notified by
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>>>>>>>>>>>>>>>>>> 06/01/23,
>>>>>>>>>>>>>>>>>> 04:51:51 PM
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> On Wed, May 31, 2023 at 10:45 AM Christoph Junghans <
>>>>>>>>>>>>>>>>>> [email protected]> wrote:
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> On Tue, May 30, 2023 at 10:46 PM Kankana Bhattacharjee <
>>>>>>>>>>>>>>>>>>> [email protected]> 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&utm_medium=signature&utm_campaign=signaturevirality11&;>
>>>>>>>>>>>>>>>>>>>> Sender
>>>>>>>>>>>>>>>>>>>> notified by
>>>>>>>>>>>>>>>>>>>> Mailtrack
>>>>>>>>>>>>>>>>>>>> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&;>
>>>>>>>>>>>>>>>>>>>> 05/31/23,
>>>>>>>>>>>>>>>>>>>> 10:12:10 AM
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> On Wed, May 31, 2023 at 10:10 AM Christoph Junghans <
>>>>>>>>>>>>>>>>>>>> [email protected]> wrote:
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> On Tue, May 30, 2023 at 10:33 PM Kankana Bhattacharjee
>>>>>>>>>>>>>>>>>>>>> <[email protected]> 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&utm_medium=signature&utm_campaign=signaturevirality11&;>
>>>>>>>>>>>>>>>>>>>>>> Sender
>>>>>>>>>>>>>>>>>>>>>> notified by
>>>>>>>>>>>>>>>>>>>>>> Mailtrack
>>>>>>>>>>>>>>>>>>>>>> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&;>
>>>>>>>>>>>>>>>>>>>>>> 05/31/23,
>>>>>>>>>>>>>>>>>>>>>> 10:02:22 AM
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> On Wed, May 31, 2023 at 9:58 AM Christoph Junghans <
>>>>>>>>>>>>>>>>>>>>>> [email protected]> wrote:
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> On Sun, May 28, 2023 at 10:13 PM Kankana
>>>>>>>>>>>>>>>>>>>>>>> Bhattacharjee <[email protected]>
>>>>>>>>>>>>>>>>>>>>>>> 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&utm_medium=signature&utm_campaign=signaturevirality11&;>
>>>>>>>>>>>>>>>>>>>>>>>> Sender
>>>>>>>>>>>>>>>>>>>>>>>> notified by
>>>>>>>>>>>>>>>>>>>>>>>> Mailtrack
>>>>>>>>>>>>>>>>>>>>>>>> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&;>
>>>>>>>>>>>>>>>>>>>>>>>> 05/29/23,
>>>>>>>>>>>>>>>>>>>>>>>> 09:41:28 AM
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> On Fri, May 26, 2023 at 9:15 PM Christoph Junghans <
>>>>>>>>>>>>>>>>>>>>>>>> [email protected]> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, May 25, 2023 at 7:23 AM Kankana
>>>>>>>>>>>>>>>>>>>>>>>>> Bhattacharjee
>>>>>>>>>>>>>>>>>>>>>>>>> <[email protected]> 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
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>>>>>>>>>>>>>>>>>>>>>>>>> > To unsubscribe from this group and stop
>>>>>>>>>>>>>>>>>>>>>>>>> receiving emails from it, send an email to
>>>>>>>>>>>>>>>>>>>>>>>>> [email protected].
>>>>>>>>>>>>>>>>>>>>>>>>> > 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
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>>>>>>>>>>>>>>>>>>>>>>>>> To unsubscribe from this group and stop receiving
>>>>>>>>>>>>>>>>>>>>>>>>> emails from it, send an email to
>>>>>>>>>>>>>>>>>>>>>>>>> [email protected].
>>>>>>>>>>>>>>>>>>>>>>>>> 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
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>>>>> Christoph Junghans
>>>>>>>>>>>>>>>>>>> Web: http://www.compphys.de
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>>> Christoph Junghans
>>>>>>>>>>>>>>>>> Web: http://www.compphys.de
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> --
>>>>>>>>>>>>> Christoph Junghans
>>>>>>>>>>>>> Web: http://www.compphys.de
>>>>>>>>>>>>>
>>>>>>>>>>>>> [image: Mailtrack]
>>>>>>>>>>>>> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&;>
>>>>>>>>>>>>> Sender
>>>>>>>>>>>>> notified by
>>>>>>>>>>>>> Mailtrack
>>>>>>>>>>>>> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&;>
>>>>>>>>>>>>> 06/02/23,
>>>>>>>>>>>>> 07:13:42 PM
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> --
>>>>>>>>>>>> Christoph Junghans
>>>>>>>>>>>> Web: http://www.compphys.de
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>> Christoph Junghans
>>>>>>>>>> Web: http://www.compphys.de
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>> 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 [email protected].
>>>>>>>>>> To view this discussion on the web visit
>>>>>>>>>> https://groups.google.com/d/msgid/votca/CAHG27e4fdqGEwaOmCf%2BHbBk%2BQ%3DAyuJ35AGn011ji6CAjdYeAgg%40mail.gmail.com
>>>>>>>>>> <https://groups.google.com/d/msgid/votca/CAHG27e4fdqGEwaOmCf%2BHbBk%2BQ%3DAyuJ35AGn011ji6CAjdYeAgg%40mail.gmail.com?utm_medium=email&utm_source=footer>
>>>>>>>>>> .
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> Christoph Junghans
>>>>>>>> Web: http://www.compphys.de
>>>>>>>>
>>>>>>> --
>>>>>> Christoph Junghans
>>>>>> Web: http://www.compphys.de
>>>>>>
>>>>>
>>>
>>> --
>>> Christoph Junghans
>>> Web: http://www.compphys.de
>>>
>>
>
> --
> Christoph Junghans
> Web: http://www.compphys.de
>
--
Join us on Slack: https://join.slack.com/t/votca/signup
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