[gmx-users] Cannot compute velocity of COM of a group of atoms

[ARNAB MUKHERJEE]

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 ?

I would highly appreciate any help.

Thank you very much,

Regards,

Arnab