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

[Justin Lemkul]

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

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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