[gmx-users] how to fix a molecule's initial configuration
mark.j.abraham at gmail.com
Thu Aug 27 08:58:54 CEST 2015
A position restraint will inhibit translation, depending on the sizes of
forces involved. Intra-molecular restraints (e.g. distances, angles) will
inhibit internal conformational changes.
On Thu, Aug 27, 2015 at 6:08 AM li he <parachuternewyork at gmail.com> wrote:
> Some one suggest "position restraint" at
> https://firstname.lastname@example.org/msg21569.html ,
> Can that restraint allow the restrainted molecule freely translate or
> rotate with a fixed configuration?
> Thank you.
> Research School of Chemistry
> 2015-08-27 11:56 GMT+08:00 li he <parachuternewyork at gmail.com>:
> > Dear gmxers,
> > I want to fix a molecule's, e.g. octanol's, initial configuration in
> > Gromacs MD simulation.
> > I find some hints at
> > https://email@example.com/msg21569.html
> > It reads that, I can apply distance restraint or use RMSD umbrella
> > sampling with PLUMED.
> > I wonder if there is smarter way to do that with GROMACS, since 6 years
> > has past
> > since that post? e.g. Does Gromacs has some utility similar to CHARMM's
> > RMSD
> > restraint ("CONS RMSD" at
> > http://www.charmm.org/documentation/c33b2/cons.html# RMSD restraints)?
> > Any suggestion or comment will be highly appreciated.
> > Thank you.
> > yours
> > xiaodong
> > Research School of Chemistry
> > ANU
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