[gmx-users] Kinetic energy of a single molecule

Justin A. Lemkul jalemkul at vt.edu
Wed Aug 10 23:59:07 CEST 2011

Size Zheng wrote:
> Hi there,
> I'm trying to find the kinetic energy for a single molecule in the system.
> I generated one individual group for the molecule in index.ndx file, and also put energygrps = ** (** is the name of the group represented the single molecule) in the .mdp file. But g_energy only allowed me to produce the total kinetic energy of the whole system. For the singe molecule, there were only LJ, Coulomb and T options.
> Is there any method to generate the kinetic energy just for the single molecule?

You can extract rotational and translational KE using g_traj.  You can also 
extract velocity information, from which calculating KE is trivial.  This 
assumes, of course, that you saved velocities in the .trr file.


> Many thanks,
> Size Zheng-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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