[gmx-users] where are the forces?
a.solernou at leeds.ac.uk
Thu Apr 2 18:19:02 CEST 2015
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?
Dr Albert Solernou
EPSRC Research Fellow,
Department of Physics and Astronomy,
University of Leeds
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