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

[ARNAB MUKHERJEE]

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