[gmx-users] velocity

[Justin Lemkul]

On 5/28/18 11:49 AM, Atila Petrosian wrote:
> Dear Mark,
> Thanks for your answer.
>
> "Only if you asked for velocity information to be written to the
> trajectory, with nstvout"
>
> Usually, I use the following lines in mdp files:
>
> nstxout = 1000
> nstvout = 1000
> nstxtcout         = 1000
> nstenergy = 1000
> nstlog = 1000
>
> But, I get only position of atoms  in time steps using VMD while I need to
> the velocity values for each time in time steps.

Inspect the contents of your .trr file to verify what you have (is what 
you "usually" do what you "always" do, or did you forget something in 
this case?) and then, if velocities are present, extract what you need 
with gmx traj.

-Justin

-- 
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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

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