[gmx-users] dummies and positional restraints

Berk Hess gmx3 at hotmail.com
Tue Aug 24 10:30:36 CEST 2004

>From: Frauke Meyer <fmeyer at iris3.simm.ac.cn>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: gmx <gmx-users at gromacs.org>
>Subject: [gmx-users] dummies and positional restraints
>Date: 24 Aug 2004 15:04:39 +0800
>it seems that currently dummy atoms can not be restraint to their
>starting position. Is there any particular reason for it, or would
>it be easy to implement (if so, where?)?
>My dummies are not defined relative to other atoms but are generated
>when mutating a ligand to dummy atoms.

The word dummies is confusing, since in Gromacs it is used to indicate
interaction sites (it would probably be better if we changed this name).

Your atoms are dummies in the usual sense, but these are treated in
Gromacs as any other atom, so position restraints should work.
If you use a posre.itp file maybe you need to add the line:
define = -DPOSRES
to you mdp file?


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