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.

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
>>>>>
>>>>>
>>>>>
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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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>>>>>>>>>>>>>>>  Sender
>>>>>>>>>>>>>>> notified by
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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
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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
>>>>>>>>>>>>>>>> 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
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>>>>>>>>>>>>>>>> To unsubscribe from this group and stop receiving emails
>>>>>>>>>>>>>>>> from it, send an email to
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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
>
> --
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