[gmx-users] position restraints
chris.neale at alum.utoronto.ca
Mon Apr 4 19:36:26 CEST 2016
What did you set for refcoord-scaling ? How are you treating volume/pressure? Please post a full .mdp file. If you want, you can simply fix the positions and not let them move at all with freezegrps etc.
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Irem Altan <irem.altan at duke.edu>
Sent: 04 April 2016 10:23
To: gmx-users at gromacs.org
Subject: [gmx-users] position restraints
I have a simulation in which I want to keep the protein coordinates fixed. I have tried using force constraints of strength 1000, 5000, and 10000. With 5000, there are about 100-150 atoms (out of ~1700) that drift more than 0.4A away from their equilibrium positions. This number increases when I use 10000. Is this expected behavior? What can I do to prevent the equilibrium positions from drifting away more than 0.4A?
Gromacs Users mailing list
* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users