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: [EMAIL PROTECTED]
> To: gmx-users@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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