[gmx-users] Temperature Calculation in MD

[Justin Lemkul]

On 2/19/16 12:19 PM, Ray Chao wrote:
> Hi, gmx users,
>
> I have a questions regarding the temperature calculation during mdrun. The
> system is periodic in x and y direction, and there a re two groups of
> molecules, polymer and water solvent. The COM motion of the system was
> removed in the mdp file. However, each group has its own COM motion. So in
> calculating the temperature of each group, e.g, gmx traj, is the COM motion
> of each group removed? Or if I want to write my own code to calculate the
> temperature, do I need to cal the COM velocity first and then get rid of it?
>

If appropriate comm-grps were used during the simulation, no additional 
correction should be necessary as the output velocities should be correct.

But the temperatures of individual groups are saved in the .edr file anyway, 
account for constraints, and are accurate over all MD steps, so it is not clear 
to me why you want to re-calculate temperatures using gmx traj.

-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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