[gmx-users] how to fix a molecule's initial configuration

li he parachuternewyork at gmail.com
Thu Aug 27 06:08:08 CEST 2015

Some one suggest "position restraint" at
https://www.mail-archive.com/gmx-users@gromacs.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://www.mail-archive.com/gmx-users@gromacs.org/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
> 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

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