[gmx-users] where are the forces?
jalemkul at vt.edu
Thu Apr 2 18:21:59 CEST 2015
On 4/2/15 12:18 PM, Albert Solernou wrote:
> I am trying to get a trajectory that include forces... but I am not sure I am
> getting it. My .mdp file has the following lines:
> nstxout = 500 ; save coordinates every 1.0 ps
> nstvout = 500 ; save velocities every 1.0 ps
> nstenergy = 500 ; save energies every 1.0 ps
> nstfout = 500 ; save forces every 1.0 ps
> nstlog = 500 ; update log file every 1.0 ps
> but because the trajectory is saved in a .trr file... it is difficult to know
> whether the forces are there or not.
> Therefore, I turn my .trr trajectory into .gro, to see what is in there:
> gmx trjconv -vel -force -s gmx.tpr -f gmx.trr -o gmx.gro
> and I expect to see 9 numbers after every atom, but there are only 6... and when
> I "trjconv" using "-novel", then only 3 numbers are there.
> So the question is: where are the forces? Were they saved at all?
gmx check -f gmx.trr will tell you.
The forces won't be written to a .gro file; those are coordinate files that hold
only coordinates or velocities. You can extract forces using gmx traj.
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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