Hi, Thank you very much for your suggestion.
By "nsteps" I meant the # of step interval between which I would record the velocity. So my simulation run has 10 million steps (200 ns) and I chose nstvout = 1000. But I was wondering is it possible to do a mdrun -rerun (changing the .mdp file), and compute the velocity for the old trajectory (.trr) file, rather than running a new simulation again? Thanks and Regards, Arnab On Wed, Aug 8, 2018 at 4:15 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 8/7/18 1:47 PM, ARNAB MUKHERJEE wrote: > >> Dear all, >> >> I have simulated a system of DNA and Protein, and I want to calculate the >> velocity of the center of mass of protein as a function of time. So I used >> the following command : >> >> gmx traj -f traj_comp.trr -s md_run-E-Field.tpr -n index.ndx -ov >> test-vel.xvg -com >> >> I have pasted below the file that it generates : >> >> # GROMACS: gmx traj, VERSION 5.0.6 >> # Executable: /applic/applications/GROMACS/5.0.6/bin/gmx >> # Library dir: /applic/applications/GROMACS/5.0.6/share/gromacs/top >> # Command line: >> # gmx traj -f traj_comp.trr -s md_run-E-Field.tpr -n index.ndx -ov >> test-vel.xvg -com >> # gmx is part of G R O M A C S: >> # >> # Georgetown Riga Oslo Madrid Amsterdam Chisinau Stockholm >> # >> @ title "Center of mass velocity" >> @ xaxis label "Time (ps)" >> @ yaxis label "Velocity (nm/ps)" >> @TYPE xy >> @ view 0.15, 0.15, 0.75, 0.85 >> @ legend on >> @ legend box on >> @ legend loctype view >> @ legend 0.78, 0.8 >> @ legend length 2 >> @ s0 legend "Protein X" >> @ s1 legend "Protein Y" >> @ s2 legend "Protein Z" >> "test-vel.xvg" 24L, 731C 24,1 >> Bot >> >> So it doesn't have the velocities. Is it due to the fact that in my .mdp >> file, I had set nstvout = 0 ? I have pasted below the initial part of my >> .mdp file >> >> title = NVT equilibration with position restraint on all solute >> (topology modified) >> ; Run parameters >> integrator = md ; leap-frog integrator >> nsteps = 5000000 ; 1 * 500000 = 500 ps >> ;nsteps = 5000 >> dt = 0.02 ; 1 fs >> ; Output control >> nstxout = 0 ; save coordinates every 10 ps >> nstvout = 0 ; save velocities every 10 ps >> nstcalcenergy = 50 >> nstenergy = 1000 ; save energies every 1 ps >> nstxtcout = 2500 >> ;nstxout-compressed = 5000 ; save compressed coordinates every 1.0 ps >> ; nstxout-compressed replaces nstxtcout >> ;compressed-x-grps = System ; replaces xtc-grps >> nstlog = 1000 ; update log file every 1 ps >> ; Bond parameters >> continuation = no ; first dynamics run >> constraint_algorithm = lincs ; holonomic constraints >> constraints = none ; all bonds (even heavy atom-H bonds) >> constrained >> ;lincs_iter = 2 ; accuracy of LINCS >> lincs_order = 4 ; also related to accuracy >> >> Is there a way I can still compute the velocities, or do I need to run the >> simulation again, putting nstvout = nsteps ? >> > > Yes, you need a non-zero value for nstvout, but you shouldn't set it to > the same value as nsteps, because then you'll only get one frame. You need > some sensible output frequency that allows you to collect relevant > statistics of the quantity of interest. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support > /Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.