[gmx-users] average force on solute
msanku65 at yahoo.com
Sat Jan 14 04:47:10 CET 2012
I am simulating a peptide in a box of water in gromacs 4.5.4 . From the trajectory, I want to compute the time-averaged force acting on the peptide.
I found g_traj tool can provide information on force upon supplying the traj.trr file and g_traj help menu also suggests that using -af option one can get the average force on a selected group.
But, I found a problem in executing the g_traj tool to calculate the average force. I find that if the .trr file do not store any coordinate ( but store only force), then the -af option actually do not work.
Since I was interested in force, in my mdp output file option,I used following settings i.e in the .trr file I only write the force.
Output frequency for coords (x), velocities (v) and forces (f)
nstxout = 0
nstvout = 0
nstfout = 5
; Output frequency for energies to log file and energy file
nstlog = 50000
nstcalcenergy = -1
nstenergy = 5000
; Output frequency and precision for .xtc file
nstxtcout = 1000
xtc_precision = 1000
But, after running the simulation, if I try to use g_traj to extract the force,using following command:
g_traj_44 -f traj.trr -s -n -af -cf
I get following warning and no average force is being written:
WARNING: No coordinate frames found for option -cv or -cf
No frames found for average force, will not write force.pdb
I wonder, why one need to have coordinate stored as well to get the average force file or there is any other work-around for this or do I really need to also store coordinates in the trr file for getting the average force.
If there is any other alternatives for getting the average force, please let me know.
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