[gmx-users] Can I change xtc-groups while continuing a simulation?

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Jul 10 21:04:11 CEST 2009

Hi Michael,

> My only idea so far sounds pretty hacky: use the original coordinates and
> mdp file to make a phony "initial.tpr" with the new xtc-groups and pass this
> phony file on to tpbconv. I'm hesitant to do this because I don't actually
> know what all is in a .tpr file and whether this would cause something to
> break without a warning.

This is close to what you should be doing:
1. Use the original .mdp file and change the xtc-grps.
2. Make a .tpr using this modified .mdp file and a coordinate file. It
doesn't really matter whether it's the first frame or another. The
positions and velocities will be read from the trajectory anyway.
3. Run tpbconv to create a run input file for the extension.

You can also use grompp to generate the run input file for the
extension, but then you'd have to change the setting for the



Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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