[gmx-users] Temperature Calculation in MD

[Justin Lemkul]

On 2/20/16 3:58 PM, Ray Chao wrote:
> Hi, Justin,
>
> Thanks for your response. By extracting temperature information out edr
> file, do you mean the "gmx enemat" command?  Actually what I was up to is

No, you need gmx energy.

> calculate the temperature development of a certain region instead of a
> group of atoms.
>

Then all you need to do is correct the gmx traj output for any constraints.  The 
velocities should already be corrected for COM motion removal, however specified 
in the .mdp file.

-Justin

-- 
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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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