[gmx-users] Cannot compute velocity of COM of a group of atoms
arnabmukherjee249 at gmail.com
Tue Aug 7 19:48:02 CEST 2018
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
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
# 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)"
@ 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
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
title = NVT equilibration with position restraint on all solute
; 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)
;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 ?
I would highly appreciate any help.
Thank you very much,
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