[gmx-users] OPLSAA parameters

[friendli]

Wow, that is great news to me.

thanks a lot.

Qiang

Berk Hess wrote:
> Yes.
>
> Gromos96 is the "inconvenient" force field in this respect (not OPLS).
> In all other common biomolecular force fields you only need to change
> the atom types, charges and masses.
>
> Berk
>
> > Date: Fri, 21 Nov 2008 18:01:15 +0800
> > From: friendli2000 at gmail.com
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] OPLSAA parameters
> >
> > I mean in mutation free energy calculations.
> >
> > for OPLSAA force field we only need to provide the mutated atom types,
> > but not need to change the [bonds], [angle] ...etc. in the topology 
> file?
> > Since in Gromos96, the parameters need to be provided for state B.
> >
> > thank you
> >
> > Qiang
> >
> >
> > Berk Hess wrote:
> > > Hi,
> > >
> > > Although optionally having the parameters in the top file
> > > might be useful, for mutation studies you don't need this,
> > > since you only need to change the atom types,
> > > you never have to give the parameters explicitly.
> > >
> > > Berk
> > >
> > > > Date: Fri, 21 Nov 2008 16:10:06 +0800
> > > > From: friendli2000 at gmail.com
> > > > To: gmx-users at gromacs.org
> > > > Subject: Re: [gmx-users] OPLSAA parameters
> > > >
> > > > Thanks Mark.
> > > >
> > > > Hope the developers can consider to output the parameters into .top
> > > file
> > > > explicitly. That would be helpful for mutation calculations at 
> least, I
> > > > think.
> > > >
> > > >
> > > >
> > > >
> > > > Mark Abraham wrote:
> > > > > friendli wrote:
> > > > >> Hi Mark,
> > > > >>
> > > > >> the atom types in .top file is opls_???, but the atom types(or
> > > > >> "name") in [bondtypes] in ffoplsaabon.itp file is C, H, CT, 
> C_3, etc.
> > > > >>
> > > > >> So we still need to look up ffoplsaanb.itp to link these two 
> "atom
> > > > >> type" (or "name"), right?
> > > > >
> > > > > OK, whatever... as I said, different force fields have different
> > > > > mechanisms.
> > > > >
> > > > > Mark
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