Regarding-Getting-itp-files:

[Kankana Bhattacharjee]

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. 

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. 

Thanks & Regards

Kankana Bhattacharjee

[Christoph Junghans]

On Thu, May 25, 2023 at 7:23 AM Kankana Bhattacharjee
<kankanabhat...@gmail.com> 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
>

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

[Kankana Bhattacharjee]

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 ? 

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[Christoph Junghans]

On Sun, May 28, 2023 at 10:13 PM Kankana Bhattacharjee <kankanabhat...@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

[Kankana Bhattacharjee]

Thank you sir. I would like to know, how can one get gromacs compatible itp file for a Coarse grained model using votca ? 

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05/31/23, 10:02:22 AM

[Christoph Junghans]

On Tue, May 30, 2023 at 10:33 PM Kankana Bhattacharjee <kankanabhat...@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.

[Kankana Bhattacharjee]

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. 

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. 

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 ?

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[Christoph Junghans]

On Tue, May 30, 2023 at 10:46 PM Kankana Bhattacharjee <kankanabhat...@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.

[Kankana Bhattacharjee]

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. 

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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[Christoph Junghans]

On Thu, Jun 1, 2023 at 5:22 AM Kankana Bhattacharjee <kankanabhat...@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 

[Kankana Bhattacharjee]

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

[Kankana Bhattacharjee]

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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[Kankana Bhattacharjee]

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 ?

Thanks & Regards

Kankana Bhattacharjee

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[Christoph Junghans]

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

---------- Forwarded message ---------
From: Christoph Junghans <jung...@votca.org>
Date: Fri, Jun 2, 2023 at 8:22 AM
Subject: Re: [votca] Regarding-Getting-itp-files:
To: Kankana Bhattacharjee <kankanabhat...@gmail.com>

On Fri, Jun 2, 2023 at 8:06 AM Kankana Bhattacharjee <kankanabhat...@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

 

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On Fri, Jun 2, 2023 at 7:27 PM Christoph Junghans <jung...@votca.org> wrote:

On Fri, Jun 2, 2023 at 7:44 AM Kankana Bhattacharjee <kankanabhat...@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 <jung...@votca.org>
Date: Fri, Jun 2, 2023 at 7:10 PM
Subject: Re: [votca] Regarding-Getting-itp-files:
To: Kankana Bhattacharjee <kankanabhat...@gmail.com>

On Fri, Jun 2, 2023 at 3:40 AM Kankana Bhattacharjee <kankanabhat...@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 

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--

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

--

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

[Kankana Bhattacharjee]

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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[Christoph Junghans]

On Fri, Jun 2, 2023 at 12:34 PM Kankana Bhattacharjee <kankanabhat...@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.

[Kankana Bhattacharjee]

Actually sir, it was asked me to prepare propane.itp (for CG).

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06/03/23, 08:29:51 AM

[Kankana Bhattacharjee]

It was asked me to generate CG propane itp file using Votca so that, I can generate for any unknown molecule

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06/03/23, 09:40:07 AM

[Christoph Junghans]

On Fri, Jun 2, 2023 at 21:00 Kankana Bhattacharjee <kankanabhat...@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.

[Kankana Bhattacharjee]

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 ?

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06/03/23, 09:45:05 AM

[Kankana Bhattacharjee]

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 ? 

I want to know how to choose which method (ibi, imc) would be accurate to give accurate structural properties? 

[Christoph Junghans]

On Fri, Jun 2, 2023 at 10:19 PM Kankana Bhattacharjee <kankanabhat...@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 Junghans]

On Sat, Jun 3, 2023 at 3:16 AM Kankana Bhattacharjee <kankanabhat...@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

[Kankana Bhattacharjee]

Thank you sir. But IBI would be for multiple propane molecules. Isn't it ? It won't be for single propane i think

[Christoph Junghans]

On Sat, Jun 3, 2023 at 9:00 AM Kankana Bhattacharjee <kankanabhat...@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.

[Kankana Bhattacharjee]

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

[Christoph Junghans]

On Sun, Jun 4, 2023, 23:15 Kankana Bhattacharjee <kankanabhat...@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.

[Kankana Bhattacharjee]

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 the
Verlet cutoff scheme.

Thanks & Regards

Kankana Bhattacharjee

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[Christoph Junghans]

On Mon, Jun 5, 2023 at 6:17 AM Kankana Bhattacharjee <kankanabhat...@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 the
Verlet 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.

[Kankana Bhattacharjee]

Ok sir. What should I do to fix it ? 

Is it true for all iterative methods ?

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[Christoph Junghans]

On Mon, Jun 5, 2023 at 7:11 AM Kankana Bhattacharjee <kankanabhat...@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 <jung...@votca.org> wrote:

On Mon, Jun 5, 2023 at 6:35 AM Kankana Bhattacharjee <kankanabhat...@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.

[Kankana Bhattacharjee]

Ok sir

[Kankana Bhattacharjee]

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 ?

Thanks and regards

Kankana Bhattacharjee
 

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06/08/23, 11:08:09 AM

[Christoph Junghans]

On Thu, Jun 8, 2023, 05:47 Kankana Bhattacharjee <kankanabhat...@gmail.com> wrote:

Dear Sir, 

I am in the process of generating CG propane.itp file. So, I obtained bond1.dist.ib and bond2.dist.ib files, angle.dist.ib from BI method. Now, to make GROMACS compatible .itp file for bonded distributions, if I use "func type 8" then, what would be other two parameters? As, acc to GROMACS, for tabulated functions (func type =8), table number and spring constant (kj/mol) has to be incorporated. For CG propane, how would I include those parameters ? 

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

Looking forward to your reply.

Thanks & Regards

Kankana Bhattacharjee

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[Christoph Junghans]

On Thu, Jun 8, 2023, 06:01 Kankana Bhattacharjee <kankanabhat...@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 <jung...@votca.org>
Date: Thu, Jun 8, 2023 at 3:27 PM
Subject: Re: [votca] Regarding-Getting-itp-files:
To: Kankana Bhattacharjee <kankanabhat...@gmail.com>

On Thu, Jun 8, 2023, 01:43 Kankana Bhattacharjee <kankanabhat...@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 

06/08/23, 03:28:24 PM

[Kankana Bhattacharjee]

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

[Kankana Bhattacharjee]

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) ?

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06/08/23, 03:57:07 PM

[Kankana Bhattacharjee]

Sir, to convert the bonded potentials into xvg format, at first I have made table_b1.xml for bond1 type and then, used the command line:

 csg_call --ia-type bond --ia-name bond1 --options table_b1.xml \ convert_potential gromacs angle.pot.ib table_b1.xvg. But, the output file: table_b1.xvg looks somewhat different from the file given in the ibi folder. Kindly provide some suggestions. 

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06/08/23, 05:04:14 PM

[Christoph Junghans]

On Thu, Jun 8, 2023, 06:29 Kankana Bhattacharjee <kankanabhat...@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.

[Kankana Bhattacharjee]

Sir, to convert the bonded potentials into xvg format, at first I have made table_b1.xml for bond1 type and then, used the command line:

 csg_call --ia-type bond --ia-name bond1 --options table_b1.xml \ convert_potential gromacs angle.pot.ib table_b1.xvg. But, the output file: table_b1.xvg looks somewhat different from the file given in the ibi folder. Kindly provide some suggestions. Sir, my table_b1.xvg is looking somewhat different from that of table_b1.xvg provided in the ibi folder. For converting into table.xvg, should "Resampling", and "Extrapolation" options also have to be followed in case of bonded distributions ?

[Christoph Junghans]

On Thu, Jun 8, 2023 at 07:54 Kankana Bhattacharjee <kankanabhat...@gmail.com> wrote:

Sir, to convert the bonded potentials into xvg format, at first I have made table_b1.xml for bond1 type and then, used the command line:

 csg_call --ia-type bond --ia-name bond1 --options table_b1.xml \ convert_potential gromacs angle.pot.ib table_b1.xvg. But, the output file: table_b1.xvg looks somewhat different from the file given in the ibi folder. Kindly provide some suggestions. Sir, my table_b1.xvg is looking somewhat different from that of table_b1.xvg provided in the ibi folder. For converting into table.xvg, should "Resampling", and "Extrapolation" options also have to be followed in case of bonded distributions ?

It depends on the system, but usually yes!

--

[Kankana Bhattacharjee]

Sir, for getting the xvg table, at first I directly created table.xml file for bond length distribution and then used csg_call command to convert the table into xvg format. But, I excluded the "Resampling" and "Extrapolation" options. Is it the correct path ? 

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06/09/23, 01:14:13 PM

[Kankana Bhattacharjee]

Dear Sir, 

For bonded distribution, if I want to convert the table into xvg format, then for the "Resampling step" the command line is, I want to know what would be the "min:step:max" options for bonded distributions ? I am not understanding this part.  

csg_resample --in table.pot --out table_resample.pot \
             --grid min:step:max

I want to know what would be the "min:step:max" options for bonded distributions ? I am not understanding this part.

Thanks & Regards

Kankana Bhattacharjee

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06/09/23, 03:08:17 PM

[Kankana Bhattacharjee]

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: angle_rad.pot.ib to angle_rad.pot.scale.3tqbn with x' = 57.2957795*x + 0
readin_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_call

Callstack:
/usr/bin/csg_call - linenumber 199
    do_external - linenumber 176 in /usr/share/votca/scripts/inverse/functions_common.sh
        /usr/share/votca/scripts/inverse/potential_to_gromacs.sh - linenumber 124
            do_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 --on-x angle_rad.pot.ib angle_rad.pot.scale.3tqbn 57.2957795 0 #
# (from tags table linearop) failed                                                                                 #
# Details can be found above                                                                                        #
#                                                                                                                   #
#####################################################################################################################
Terminated


But, for bonded distributions table.xvg files generated. For angle potential, not getting the table and not able to figure out the error. 

Kindly help me with this.

Thanks & Regards

Kankana Bhattacharjee 

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06/09/23, 04:02:39 PM

[Kankana Bhattacharjee]

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.   

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06/09/23, 04:58:12 PM

[Kankana Bhattacharjee]

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 <jung...@votca.org> wrote:

On Fri, Jun 9, 2023 at 5:29 AM Kankana Bhattacharjee <kankanabhat...@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

[Kankana Bhattacharjee]

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. 

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06/12/23, 03:03:46 PM

[Christoph Junghans]

On Mon, Jun 12, 2023, 03:30 Kankana Bhattacharjee <kankanabhat...@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. 

[Christoph Junghans]

On Mon, Jun 12, 2023, 03:37 Kankana Bhattacharjee <kankanabhat...@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.

[Kankana Bhattacharjee]

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: 0.000000

0.229153 0.343730

How can I fix this issue i.e, equally spacing x values ? 

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06/14/23, 11:46:13 AM

[Christoph Junghans]

On Wed, Jun 14, 2023, 00:17 Kankana Bhattacharjee <kankanabhat...@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: 0.000000

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?

[Kankana Bhattacharjee]

Sir, now angle_a1.xvg worked for gmx mdrun option. 

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 ? 

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06/15/23, 10:21:58 AM

[Christoph Junghans]

On Wed, Jun 14, 2023, 22:55 Kankana Bhattacharjee <kankanabhat...@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.

[Kankana Bhattacharjee]

Ok. Thank you sir.

I would like to compare the bonded distributions from AA and CG simulation. I have performed simulation using GROMACS software. How can I do this job ? 

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06/16/23, 05:34:12 PM

[Christoph Junghans]

On Fri, Jun 16, 2023, 06:07 Kankana Bhattacharjee <kankanabhat...@gmail.com> wrote:

Ok. Thank you sir.

I would like to compare the bonded distributions from AA and CG simulation. I have performed simulation using GROMACS software. How can I do this job ? 

You could run csg_stat on both trajectories. Use a 1:1 mapping file for the CG case and a normal mapping file for the AA simulation.

[Kankana Bhattacharjee]

Thank you sir for your kind help. 

I converted atomistic trajectory into CG trajectory using csg_map tool. And, I have CG trajectory from CGMD run.  So, if I use csg_stat tool, then what should be the exact command line option for each atomistic and CG runs:

If I want to calculate bonded distribution for AA run: then, csg_stat --trj traj-mapped.xtc (atomistic trajectory mapped into CG) then, what would be the other options for getting bond length, angle distribution and the same thing for CGMD run. 

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06/16/23, 07:51:54 PM

[Christoph Junghans]

On Fri, Jun 16, 2023 at 8:32 AM Kankana Bhattacharjee <kankanabhat...@gmail.com> wrote:

Thank you sir for your kind help. 

I converted atomistic trajectory into CG trajectory using csg_map tool. And, I have CG trajectory from CGMD run.  So, if I use csg_stat tool, then what should be the exact command line option for each atomistic and CG runs:

If I want to calculate bonded distribution for AA run: then, csg_stat --trj traj-mapped.xtc (atomistic trajectory mapped into CG) then, what would be the other options for getting bond length, angle distribution and the same thing for CGMD run. 

csg_stat --top topol.tpr --trj  traj-mapped.xtc --options settings.xml --cg 1to1map.xml.

Here is an example for 1to1 map for hexane:

https://github.com/votca/votca/blob/master/csg-tutorials/hexane/ibi_all/hexane_cg.xml

[Kankana Bhattacharjee]

Thank you sir. I would like to know, why 1 to 1 mapping scheme is used ? And, for getting bonded distribution (bond length 1, bond length 2) from AA run, how settings.xml file would be helpful as that file is having nonbonded interaction terms. I would like to visualise bond length and angle distribution. 

In case of CG run, what would be the options ? 

[Christoph Junghans]

On Fri, Jun 16, 2023 at 10:35 Kankana Bhattacharjee <kankanabhat...@gmail.com> wrote:

Thank you sir. I would like to know, why 1 to 1 mapping scheme is used ?

You need the mapping file to define the bonds, not all topology files had that information hence votca reads it from the mapping file.

And, for getting bonded distribution (bond length 1, bond length 2) from AA run, how settings.xml file would be helpful as that file is having nonbonded interaction terms.

If you don’t want to average over the bonds you will have to list bond1 and bond2 separately in the settings and mapping file.

If you don’t need the non-bonded distributions just drop these sections from the file.

I would like to visualise bond length and angle distribution. 

In case of CG run, what would be the options ? 

pick your favorite tool, matplotlib or gnuplot is what most people are using!

Christoph 

[Christoph Junghans]

PS: gromacs has a tool to calculate bond lengths as well.

[Kankana Bhattacharjee]

Thanks a lot sir. I would like to get the bonded distributions from csg_stat tool. And, I want to average the  bond lengths. dont want nonbonded distributions. So, what would be the format of settings file to include the bond part so that, I can get average bond length distribution.

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06/17/23, 08:54:09 AM

[Kankana Bhattacharjee]

Sir, from single propane (atomistic)  run, I obtained bonded distributions as (bond1.dist.ib, bond2.dist.ib and angle.dist.ib) using csg_boltzmann tool.  Should I have to compare these distributions with Coarse grained MD simulations ? I am not understanding how to compare for bonded distributions with Coarse grained runs ? 

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06/17/23, 12:50:14 PM

[Kankana Bhattacharjee]

Sir, I converted the atomistic trajectory into CG trajectory using the command line:

csg_map --top topol.tpr --trj traj-10ns.trr --cg propane.xml --out traj-mapped.xtc

Then, using csg_stat how will I compute the bonded distributions I mean which settings.xml file has to be used and for AA run, which mapping file has to be used ? 

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06/17/23, 03:01:28 PM

[Christoph Junghans]

On Fri, Jun 16, 2023 at 9:28 PM Kankana Bhattacharjee <kankanabhat...@gmail.com> wrote:

Thanks a lot sir. I would like to get the bonded distributions from csg_stat tool. And, I want to average the  bond lengths. dont want nonbonded distributions. So, what would be the format of settings file to include the bond part so that, I can get average bond length distribution.

Then just make one entry for a bond in settings.xml and drop the non-bonded sections.

Similar to https://github.com/votca/votca/blob/master/csg-tutorials/hexane/ibi_all/settings.xml#L4_L15

[Christoph Junghans]

On Sat, Jun 17, 2023 at 8:47 AM Kankana Bhattacharjee <kankanabhat...@gmail.com> wrote:

Sir, i performed single atomistic and XG trajectory. Now i want to compare bonded distributions in both runs. Using csg_boltzmann i obtained bond.dist.ib and angle.dist.in plot. Now, should I have to compare this with CG run using csg_boltzmann tool by providing 1to 1 mapping file of propane and settings file ? 

csg_boltzmann doesn't need a 1:1 mapping, that is only needed when using csg_stat.

If i use csg_stat then, which settings file I have to use ?

You need a settings file that contains the information about the bonded interactions. As I said earlier the propane tutorials doesn't have that, but you can adopt the file from the hexane tutorial, see:

https://github.com/votca/votca/tree/master/csg-tutorials/hexane/ibi_all

Because there is one settings file in propane/atomistic directory containing nonbonded information only. How bonded distributions i have to include there. Kindly help me with this.

As I said earlier, just add a block like this:

https://github.com/votca/votca/blob/master/csg-tutorials/hexane/ibi_all/settings.xml#L4_L15

On Sat, Jun 17, 2023, 19:50 Christoph Junghans <jung...@votca.org> wrote:

On Sat, Jun 17, 2023 at 1:23 AM Kankana Bhattacharjee <kankanabhat...@gmail.com> wrote:

Sir, from single propane (atomistic)  run, I obtained bonded distributions as (bond1.dist.ib, bond2.dist.ib and angle.dist.ib) using csg_boltzmann tool.  Should I have to compare these distributions with Coarse grained MD simulations ? I am not understanding how to compare for bonded distributions with Coarse grained runs ? 

I am not sure what you are trying to achieve but for a structure-based CG model you want the AA and CG distributions to look the same, hence you want to compare them.

[Kankana Bhattacharjee]

Ok. Thank you sir

[Kankana Bhattacharjee]

Sir, for AA simulation, options would be like this :

csg_stat --top topol.tpr --trj traj-mapped.xtc --cg propane.xml  (normal mapping fie) --options settings.xml 

And, for CGMD run,

csg_stat --top topol.tpr (CG one) --trj CG.xtc --cg 1to 1 mapping.xml --options settings.xml 

Is it correct sir ?

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06/19/23, 09:31:40 AM

[Christoph Junghans]

On Sun, Jun 18, 2023 at 10:04 PM Kankana Bhattacharjee <kankanabhat...@gmail.com> wrote:

Sir, for AA simulation, options would be like this :

csg_stat --top topol.tpr --trj traj-mapped.xtc --cg propane.xml  (normal mapping fie) --options settings.xml 

With a mapping file, you want to use the original (AA / not-mapped) trajectory. 

You can decide 1) use csg_stat on AA traj with a mapping file,  or 2) map the traj first and then use the same command as for the CG runs.

And, for CGMD run,

csg_stat --top topol.tpr (CG one) --trj CG.xtc --cg 1to 1 mapping.xml --options settings.xml 

that is right!

[Kankana Bhattacharjee]

But sir, after executing the command line: 

 csg_stat --top topol.tpr --trj traj-mapped.xtc --cg propane.xml --options settings.xml

Error is: 

an error occurred:
settings.xml: Parse error at line 35
no element found: iostream error

I am not able to figure out the error. Also, in case of propane 2 bond is present, should I have to include 2 bonds in the settings file for getting average bond distributions from the atomistic run. I am attaching the settings.xml file here. Kindly help me with this. 

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06/19/23, 10:34:54 AM

[Kankana Bhattacharjee]

Also sir, I am having one doubt, previously I obtained bond, angle distributions using csg_boltzmann tool from the atomistic run and now, should I have to only use CG trajectory for comparing the distributions i.e, using only csg_stat tool. 

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06/19/23, 10:44:34 AM

[Kankana Bhattacharjee]

Sir, I am using gmx angle and gmx distance for computing bond length and angle distributions from the AA and CGMD runs. For doing angle distributions from AA run, at first converted the atomistic trajectory into CG trajectory (traj-mapped trajectory). 

Ist command line:

csg_map --top topol.tpr --trj traj-10ns.trr --cg propane.xml --out traj-mapped.xtc

Then, made the index file for angle distribution as: (index file making is same in both AA and CGMD runs)

[ angles ] 

1 2 3 for both aa and cgmd runs. 

Then, used the command line in  gromacs : 

gmx angle -f traj-mapped.xtc -n aa-angle1.ndx -od aa-angle-dist.xvg  

But, I am not understanding how to do bond length distribution in both AA and CGMD runs. I mean, how to make the index file for bond length distribution in both AA and CGMD runs. Using gmx distance I am trying to do this job. But, not understanding how to make index file for the same. 

Kindly help me with this. 

[Christoph Junghans]

On Sun, Jun 18, 2023 at 11:07 PM Kankana Bhattacharjee <kankanabhat...@gmail.com> wrote:

But sir, after executing the command line: 

 csg_stat --top topol.tpr --trj traj-mapped.xtc --cg propane.xml --options settings.xml

Error is: 

an error occurred:
settings.xml: Parse error at line 35
no element found: iostream error

This error means you have a syntax error in your settings.xml, I think you are missing the </cg> tag at the every end. 

I am not able to figure out the error. Also, in case of propane 2 bond is present, should I have to include 2 bonds in the settings file for getting average bond distributions from the atomistic run. I am attaching the settings.xml file here. Kindly help me with this. 

If you want to average over both bonds then you should list only one bond section  in settings.xml and make sure you list both bonds in the mapping file on one block, similar to what we did for hexane:

https://github.com/votca/votca/blob/master/csg-tutorials/hexane/ibi_all/hexane_cg.xml#L29_L30

[Christoph Junghans]

On Sun, Jun 18, 2023 at 11:17 PM Kankana Bhattacharjee <kankanabhat...@gmail.com> wrote:

Also sir, I am having one doubt, previously I obtained bond, angle distributions using csg_boltzmann tool from the atomistic run and now, should I have to only use CG trajectory for comparing the distributions i.e, using only csg_stat tool. 

As I said above it is your choice, csg_boltzmann and csg_stat can both calculate distributions. csg_boltzmann is more manual and only works for smaller trajectories, while csg_stat has no interactive interface and can process large systems as well. 

[Christoph Junghans]

On Mon, Jun 19, 2023 at 5:25 AM Kankana Bhattacharjee <kankanabhat...@gmail.com> wrote:

Sir, I am using gmx angle and gmx distance for computing bond length and angle distributions from the AA and CGMD runs. For doing angle distributions from AA run, at first converted the atomistic trajectory into CG trajectory (traj-mapped trajectory). 

Ist command line:

csg_map --top topol.tpr --trj traj-10ns.trr --cg propane.xml --out traj-mapped.xtc

Then, made the index file for angle distribution as: (index file making is same in both AA and CGMD runs)

[ angles ] 

1 2 3 for both aa and cgmd runs. 

Then, used the command line in  gromacs : 

gmx angle -f traj-mapped.xtc -n aa-angle1.ndx -od aa-angle-dist.xvg  

But, I am not understanding how to do bond length distribution in both AA and CGMD runs. I mean, how to make the index file for bond length distribution in both AA and CGMD runs. Using gmx distance I am trying to do this job. But, not understanding how to make index file for the same. 

Sorry this is more a question for the gromacs mailing list.

Christoph

[Kankana Bhattacharjee]

Thanks Sir

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06/19/23, 11:46:02 PM

[Kankana Bhattacharjee]

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) ? 

[Christoph Junghans]

On Tue, Jun 20, 2023 at 4:07 AM Kankana Bhattacharjee <kankanabhat...@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

[Kankana Bhattacharjee]

Yes sir.

[Christoph Junghans]

On Tue, Jun 20, 2023 at 9:57 PM Kankana Bhattacharjee <kankanabhat...@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 

[Kankana Bhattacharjee]

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. 

[Christoph Junghans]

On Wed, Jun 21, 2023 at 7:21 AM Kankana Bhattacharjee <kankanabhat...@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

[Kankana Bhattacharjee]

Sir, I have attached the slides for inverted bond length distributions for the two bonds

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06/21/23, 08:57:00 PM

[Kankana Bhattacharjee]

Sir, I am using gromacs 2022 version. But, tabulated potentials are supported in GROMACS 2019 version. Is discrepancy because of GROMACS version ?

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06/22/23, 10:37:36 AM

[Christoph Junghans]

On Wed, Jun 21, 2023 at 9:27 AM Kankana Bhattacharjee <kankanabhat...@gmail.com> wrote:

Sir, I have attached the slides for inverted bond length distributions for the two bonds

Hmm, I think you will need to do some smoothing and extrapolation of those potentials.

Try to get something out like this:

https://github.com/votca/votca/blob/master/csg-tutorials/propane/ibi/table_b1.xvg

[Christoph Junghans]

On Wed, Jun 21, 2023 at 11:09 PM Kankana Bhattacharjee <kankanabhat...@gmail.com> wrote:

Sir, I am using gromacs 2022 version. But, tabulated potentials are supported in GROMACS 2019 version. Is discrepancy because of GROMACS version ?

Maybe. But you are still using tables for the bonds, right? 

[Kankana Bhattacharjee]

Sir, tables for both the bond and angle.

[Christoph Junghans]

On Thu, Jun 22, 2023 at 7:35 AM Kankana Bhattacharjee <kankanabhat...@gmail.com> wrote:

Sir, tables for both the bond and angle.

Ok, I don't think much would change between gromacs 2019 and 2022 for such a simple system... but of course I don't know.

You could use our docker container that one has gromacs-2019 in it.

Download docker from https://www.docker.com/ and then run the votca/votca container.

But honestly if you only want to do BI, you can easily do that by hand without VOTCA. 

Use gmx to calculate the distribution and then invert them following Equ 6 of http://dx.doi.org/10.1021/ct900369w, that's all.

Christoph

[Kankana Bhattacharjee]

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 ?

Your suggestions would be much appreciated.

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06/27/23, 03:39:45 PM

[Christoph Junghans]

On Tue, Jun 27, 2023, 04:13 Kankana Bhattacharjee <kankanabhat...@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

[Kankana Bhattacharjee]

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

[Christoph Junghans]

On Tue, Jun 27, 2023, 05:18 Kankana Bhattacharjee <kankanabhat...@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.

[Kankana Bhattacharjee]

Sir, what would be the typical force constant value in case of angle for CG propane if I Don't use tabulated functional form?

[Christoph Junghans]

On Tue, Jun 27, 2023 at 9:57 PM Kankana Bhattacharjee <kankanabhat...@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.

[Kankana Bhattacharjee]

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 ? 

[Christoph Junghans]

On Fri, Jun 30, 2023, 02:36 Kankana Bhattacharjee <kankanabhat...@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.

[Kankana Bhattacharjee]

Ok. Thanks Christoph.