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.