[gmx-users] where are the forces?
a.solernou at leeds.ac.uk
Thu Apr 2 18:24:54 CEST 2015
That was fast!!
Thanks Justin, the forces are effectively there and I am getting them out.
On 04/02/2015 05:21 PM, Justin Lemkul wrote:
> 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.
Dr Albert Solernou
EPSRC Research Fellow,
Department of Physics and Astronomy,
University of Leeds
More information about the gromacs.org_gmx-users