Generating-CG-itp-files:

[Kankana Bhattacharjee]

Dear Sir,

I am practicing the votca tutorial for propane molecule. I am trying to generate .itp file of CG propane. For that I used the command line:

csg_gmxtopol --topol.tpr --cg propane.xml --out cg.top, then obtained the top file. But, there bond length and angle value between the beads is not mentioned. How to get those bonded information of the beads so that, I can run GROMACS simulation of the CG system ? 

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

Thanks & Regards

Kankana Bhattacharjee

[Christoph Junghans]

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

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

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

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

Christoph

>
>
> Thanks & Regards
> Kankana Bhattacharjee
>

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