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
>
>
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>  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
>>
>>
>>
>>
>>>
>>>
>>>
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>>>  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]
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>>>>>>  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.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
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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
>>>>>>>>
>>>>>>>>
>>>>>>>>
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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
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
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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
>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
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>>>>>>>>>>>>  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]
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>>>>>>>>>>>>>>  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]
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>>>>>>>>>>>>>>>>  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 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/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
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>>>>>>>>>>>>>>>>> To unsubscribe from this group and stop receiving emails
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>>>>>>>>>>>>>>>>> To view this discussion on the web visit
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>>>>>>>>>>>>>>>>> .
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>> 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
>>>>>
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>>>>>  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
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>> .
>>
>

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

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