Hi,
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.
Thanks
Sanku
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