[gmx-users] difference between gmx energy and gmx traj

[Justin Lemkul]

On 2/9/16 5:24 PM, Ray Chao wrote:
> Hi, All,
>
> I ran a NVT simulation for a water sphere with position restraint. The
> TIP4P water model was used. I tried to relax the system at temperature of
> 300K.  After the simulation, I used gmx energy to cal the system
> temperature and it is around 300K. However, when I tried to use gmx traj to
> extract the temperature from "SOL" group, the temperature is always half of
> that calculated from gmx energy. Is there any difference between these two
> commands? Or is there any other way to determine the temperature of each
> group?
>

You need to account for constraints.  See the help text of gmx traj and previous 
discussions on this topic in the archive.

-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

==================================================