[CP2K:4956] Re: gmx2gromos

leila salimi leila... at gmail.com
Wed Feb 19 13:47:20 UTC 2014

Dear All,

Do you have any suggestion for my question?

Thanks very much,

On Tue, Feb 18, 2014 at 8:49 PM, leila <leila... at gmail.com> wrote:

> 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
> On Wednesday, August 27, 2008 9:03:02 PM UTC+2, Axel wrote:
>> On Aug 27, 11:47 am, Laino Teodoro <teodor... at 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.
>> >
>> > Teo
>> >
>> > On 27 Aug 2008, at 17:36, Ewald Pauwels wrote:
>> >
>> > > 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?
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