[gmx-users] OPLSAA parameters
gmx3 at hotmail.com
Fri Nov 21 09:02:59 CET 2008
In 3 C and O are not atom names, but bonded atom types.
OPLS has non-bonded atom types opls_???
which in turn have bonded atom types.
There are far less bonded atom types then there
are non-bonded atom types.
Different force fields are set up in different ways.
OPLS is simple in some respects and more complex
in this respect (this is not a Gromacs but an OPLS issue).
> Date: Fri, 21 Nov 2008 14:32:25 +0800
> From: friendli2000 at gmail.com
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] OPLSAA parameters
> So to obtain the parameters(e.g. bonds) in topology file,
> 1, read bond atoms in .top (e.g. 1 2)
> 2, find atom types of the bond atoms in .top (e.g. oplsaa_235,
> 3, find atom names of the above atom types in ffoplsaanb.itp (e.g. C, O)
> 4, check parameters in ffoplsaabon.itp
> Is that right? why it comes to such complex in GMX?
> Mark Abraham wrote:
> > friendli wrote:
> >> In ffoplsaa.rtp, I find atom name CG and OG1 corresponds to atom type
> >> opls_235 and opls_236.
> >> While in oplsaanb.itp, the atom type opls_235 and opls_236
> >> corresponds to atom "name"(as display in titles in oplsaanb.itp) C
> >> and O.
> >> why there are two different "name"s for the same atom? what is the
> >> difference?
> > Different force fields use the machinery differently, but I can't
> > think of a purpose for the atom name field in the parameter .itp file
> > if there is a separate atom type.
> > The purpose of atom names, residue names and residue numbering in a
> > pre-pdb2gmx structure file is to look up the right atom types in the
> > .rtp file and write them to the .top file. The purpose of the atom
> > types in the .top file is to look up the right parameters in the .itp
> > file when running grompp. At that point, atom names are probably just
> > for user convenience.
> > Mark
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