[gmx-users] all atom force field

Kai Zhuang kai.zhuang at gmail.com
Tue Jun 21 19:51:28 CEST 2005

why do you have to use gromacs force field?
it's not suggested to use that one because it's outdated.
use GROMOS96 43a2 Forcefield instead, it is Gromos96 with improved alkane


On 6/21/05, 이 선주 <sunnytov at hotmail.com> wrote:
> Hello All!
> I am trying to parameterize a small molecule so that I can do the md
> simulation it with lipid bilayer.
> The problem I have is that I have to use the gromax united force field for
> the lipid bilayer part but I need
> all atom force field for the small molecule. Especially my small molecule
> has a short alkane chain of
> three carbon atoms. So now I had to introduce new atom types for alkane
> carbon and hydrogen atoms
> to the gromax force field. I adopted parameters from oplass force field and
> ffgmx2 force field and modified ffgmx.atp, ffgmxnb.itp and ffgmxbon.itp
> files and finally could minimize the molecule
> and start md simulation, but after several ps the molecule blew up.
> I started the md simulation from a single minized structure at very low
> temperature and in vacuo.
> I think the parameters were not accordant with the parameter sets in ffgmx
> force field.
> Here is my question. Is it a good or ever plausible idea to introduce new
> atom types
> into the gromax force field and to simulate alkane hydrogen explicitly?
> If yes, can you suggest me ways to get the right parameters for new atoms
> types?
> If not, do I have to generate rtp file for my small molecule and use dummy
> atoms for hydrogen atoms? In this case, should I use ffgmx2 force field or
> still can I use ffgmx force field?
> I am looking forward helps.
> Thanks in advance
> Sunjoo
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Kai Zhuang
BioMedical Engineering @ University of Toronto
kai dot zhuang at gmail dot com
kai.zhuang at gmail.com

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