[gmx-users] temperatures of residues

[Justin Lemkul]

On 1/15/16 11:28 PM, Ali Mohyeddin wrote:
> Dear all,
>
> I am going to calculate the temperature distribution inside a protein
> (temperatures of residues). Is there any command in gromacs to do that? Any
> suggestion is appreciated.
>

gmx traj can calculate it from a .trr in which you have saved velocities.  You 
will need suitable index groups for the residues and you will need to correct 
the output for any constraints used.

-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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