[gmx-users] No velocity and transitional kinetic energy calculated from gmx traj

[Bui, Tai]

Hi Justin,

Thank you very much for your answer. I figured out that I did not save velocity during my simulation. Now it's ok. 

Best,

Tai

-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Justin Lemkul
Sent: 02 July 2016 12:42
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] No velocity and transitional kinetic energy calculated from gmx traj



On 7/1/16 4:43 AM, Bui, Tai wrote:
> Dear Gromacs users,
>
> I want to calculate velocity and transitional kinetic energy of one molecule (CH4 united atom) during the simulation. I tried to use gmx traj, however it gave me 2 output files without any results for the velocity and the energy I wanted. The command I did is:
>
> gmx traj -f out.trr -s input.tpr -ov v.xvg -ekt etrans.xvg
>
> I don't know what I did wrong here. Do you have any suggestion? I appreciate your help!
>

Did you actually save velocities during the run with nstxout > 0? Use gmx check to be sure you actually have what you need.

-Justin

--
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul

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