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

[Justin Lemkul]

On 8/8/18 10:33 AM, ARNAB MUKHERJEE wrote:
> 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?

The -rerun function is for re-evaluating energies of provided 
configurations. I don't think it provides any reliable estimate of 
velocities.

-Justin

> 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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-- 
==================================================

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

==================================================