gmx2gromos

[Ewald Pauwels]

Dear all,

At the moment, I'm experimenting a bit with FIST to do simulations on
proteins using the GROMOS force field. Looking at regtest-8, e.g.
G96.inp and related files, I wonder how the parameter and connectivity
files were made?
The title section of the ala-wat.gtop file mentions:
'TITLE
'topology generated by gmx2gromos
'from file new.tpr on Thu Jun 22 13:22:41 2006
'Protein in water
'END

I get the feeling that these files were somehow converted from gromacs
format. Is this program (or another conversion utility) available
somewhere? Or, alternatively, is it described how the G96 topology and
connectivity should be structured?

Sincerely,
Ewald

[Laino Teodoro]

Ciao Ewald,

gmx2gromos is not part of the cp2k distribution. Have no idea how those

files where created (maybe one of the guy that did it will reply here with 

more informations). Anyway since you want to use GROMOS FF calculations

if you already have them you should not need any additional file or conversion.

If you don't have them please refer to the GROMOS website.. 

or to the GROMACS website (maybe there you will find also information how

to convert the two formats one in the other).

Teo

[Axel]

On Aug 27, 11:47 am, Laino Teodoro <teodoro.la...@gmail.com> wrote:
> Ciao Ewald,
>
> gmx2gromos is not part of the cp2k distribution. Have no idea how those
> files where created (maybe one of the guy that did it will reply here
> with more informations). Anyway since you want to use GROMOS FF calculations

gmx2gromos was started by me when i was still in bochum
with the intent to use gromacs tools to build OPLS/AA
topologies for qm/mm and then run them with CPMD, which
requires gromos format topology files.

> if you already have them you should not need any additional file or
> conversion.
> If you don't have them please refer to the GROMOS website..

please note that the format in cp2k (and cpmd) corresponds to
the gromos 96 file format. a minimal and reverse engineered
description is also in the qm/mm section of the cpmd manual.
perhaps somebody near you has an old gromos documentation
collecting dust on a shelf.

> or to the GROMACS website (maybe there you will find also information
> how to convert the two formats one in the other).

nope. since the gromacs tpr file is binary, you need to use
gromacs library functions to access to contents and convert them
to gromos. reading the gromos documentation is the better way.
that being said, you don't need to write gromos format topologies
to use the gromos force field. you just need the parameters and a
topology file in a format that is readable by cp2k.

cheers,
axel.

[leila]

Dear Axel, 

I am doing Fist simulation with cp2k but I want to use the Gromos and OPLS/AA force filed parameters. Can I use your program gmx2gromos to convert gromacs files to the files that is readable for cp2k like in regtest-8 ?

One of my problem is that I have CH3 in my molecule and in gromos force filed partial charges for CH3 is 0 (as the united atom of the GROMOS forcefield) and It doesn't consider single H atoms,  but "includes" these H atoms

into the C atoms. That means that the CH3 group is just one LJ-bead in the GROMOS forcefield.

How I can implement this type of parameters in CP2K format?

Thanks very much and Kind Regards, 

Leila

[leila salimi]

Dear All, 

Do you have any suggestion for my question?

Thanks very much, 

Leila

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