[gmx-users] Saving trajectories of a particular group within the system

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Dec 23 11:53:24 CET 2008

Hi Wade,

> I intend to generate only the trajectories of my protein alone,
> without outputing trajectories of the solvents. This is since the
> output files can get really massive. So looking at the manual, I've
> inserted the line: "xtc_grps = Proteins" into the .mdp input file and
> did a short simulation to try it out.

"Proteins" is not a standard group, but from the paste of your .mdp
file it seems you used "Protein" instead, which is correct. Please try
to stick to literal representations.
The real problem seems to be that "xtc_grps" is not correct, but
should be replaced with "xtc-grps". This almost brought me to shouting
"RTFM",  but a quick glance showed that the manual disagrees with the
source code at this point (both for 3.3.1 and 4.0.2). So, not your
fault, really, but the correct line should read

xtc-grps = Protein



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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