<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; ">Hi,</div><div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; "> 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. </div><div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; ">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.</div><div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; ">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.</div><div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; "><br></div><div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; ">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.</div><div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; "><br></div><div><div><font face="'times new roman', 'new york', times, serif"> Output frequency for coords (x), velocities (v) and forces (f)</font></div><div><font face="'times new roman', 'new york', times, serif">nstxout = 0</font></div><div><font face="'times new roman', 'new york', times, serif">nstvout
= 0</font></div><div><font face="'times new roman', 'new york', times, serif">nstfout = 5</font></div><div><font face="'times new roman', 'new york', times, serif">; Output frequency for energies to log file and energy file</font></div><div><font face="'times new roman', 'new york', times, serif">nstlog = 50000</font></div><div><font face="'times new roman', 'new york', times, serif">nstcalcenergy = -1</font></div><div><font face="'times new roman', 'new york', times, serif">nstenergy = 5000</font></div><div><font face="'times new roman', 'new york', times, serif">; Output frequency and precision for .xtc file</font></div><div><font face="'times new roman', 'new york', times, serif">nstxtcout
= 1000</font></div><div><font face="'times new roman', 'new york', times, serif">xtc_precision = 1000</font></div><div><font face="'times new roman', 'new york', times, serif"><br></font></div><div><font face="'times new roman', 'new york', times, serif">But, after running the simulation, if I try to use g_traj to extract the force,using following command:</font></div><div><font face="'times new roman', 'new york', times, serif"> g_traj_44 -f traj.trr -s -n -af -cf</font></div><div><font face="'times new roman', 'new york', times, serif"><br></font></div><div><font face="'times new roman', 'new york', times, serif">I get following warning and no average force is being written:</font></div><div><font face="'times new roman', 'new york', times, serif"><br></font></div><div><font face="'times new roman', 'new york', times, serif"><div>WARNING: No coordinate frames found for
option -cv or -cf</div><div><br></div><div>No frames found for average force, will not write force.pdb</div><div><br></div><div>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.</div><div><br></div><div><br></div><div>If there is any other alternatives for getting the average force, please let me know.</div><div><br></div><div>Thanks</div><div>Sanku</div></font></div></div></div></body></html>