[gmx-users] RE: all atom force field for a small molecule

이 선주 sunnytov at hotmail.com
Tue Jun 21 22:48:10 CEST 2005

I am using gmx force field updated by Bert de Groot in 2003. 
This force field contains atom types I need to simulate SOPC bilayer.


>Date: Tue, 21 Jun 2005 13:51:28 -0400
>From: Kai Zhuang <kai.zhuang at gmail.com>
>Subject: Re: [gmx-users] all atom force field
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <66c8725f050621105154e661a9 at mail.gmail.com>
>Content-Type: text/plain; charset=EUC-KR
>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it's not suggested to use that one because it's outdated.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 
> > the lipid bilayer part but I need
> > all atom force field for the small molecule. Especially my small 
> > 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 
> > 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 
> > force field.
> >
> > Here is my question. Is it a good or ever plausible idea to introduce 
> > 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 
> > types?
> > If not, do I have to generate rtp file for my small molecule and use 
> > atoms for hydrogen atoms? In this case, should I use ffgmx2 force field 
> > still can I use ffgmx force field?
> >
> > I am looking forward helps.
> >
> > Thanks in advance
> > Sunjoo
> >
> > _________________________________________________________________
> > 고.. 감.. 도.. 사.. 랑.. 만.. 들.. 기.. MSN 러브
> > http://www.msn.co.kr/love/
> >

싸게 싸게 MSN공동구매   

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