[gmx-users] OPLSAA parameters

[friendli]

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
> > > _______________________________________________
> > > gmx-users mailing list gmx-users at gromacs.org
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > Please search the archive at http://www.gromacs.org/search before
> > > posting!
> > > Please don't post (un)subscribe requests to the list. Use the www
> > > interface or send it to gmx-users-request at gromacs.org.
> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> > >
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before 
> posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
> ------------------------------------------------------------------------
> Express yourself instantly with MSN Messenger! MSN Messenger 
> <http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/>
> ------------------------------------------------------------------------
>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php