[gmx-users] Cannot compute velocity of COM of a group of atoms
jalemkul at vt.edu
Wed Aug 8 16:34:52 CEST 2018
On 8/8/18 10:33 AM, ARNAB MUKHERJEE wrote:
> 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
> Thanks and Regards,
> 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
>>> 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)
>>> ;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 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
>> Gromacs Users mailing list
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Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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