[gmx-users] dummies and positional restraints

Berk Hess gmx3 at hotmail.com
Tue Aug 24 12:25:42 CEST 2004

>From: Frauke Meyer <fmeyer at iris3.simm.ac.cn>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Subject: RE: [gmx-users] dummies and positional restraints
>Date: 24 Aug 2004 18:23:09 +0800
> > 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?
> >
>But it does not. I tested by running two simulations that only differ
>in that the ligand consists of normal atoms in one and of dummy atoms in
>the other one (atoms just differ in charge and LJ parameters).
>The dummy ligand moves, the 'normal' ligand does not.

There is no difference in free-energy no/yes and lambda
between the two simulations?

Because the position restraint force constants for topology B
might be zero. grompp will warn about this.
In that case you would need to add 1000 1000 1000
to each position restraint.


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