[gmx-users] Calculating intermolecular water interactions

Justin Lemkul jalemkul at vt.edu
Tue Oct 21 14:28:31 CEST 2014

On 10/20/14 8:57 PM, Jackson Chief Elk wrote:
> Hello, I need to calculate the intermolecular interaction energy for water
> confined to a micro cavity I simulated in a biphasic water-bromobutane
> system.  What I need to do is calculate the interaction energies ONLY for
> water that is within 0.4nm from the center-of-mass of the micro-cavity.  Has
> anybody attempted to do this on their simulation data? I don't know where to
> start because g_energy does not give me what I need, and the documentation
> and examples of g_enemat are suboptimal. Jackson

g_enemat won't do this for you, anyway.  It's designed to just plot matrices of 
existing data, derived from energygrps, which won't work for you.

Since I'm assuming the group isn't necessarily the same size in each frame, the 
only way I can think to do this is somewhat complex.

1. Use g_select to write out index groups for each frame in the trajectory to 
identify the waters in the cavity.
2. Write out the corresponding frames from the trajectory to individual files.
3. Set the waters identified by g_select and whatever other components as 
energygrps in an .mdp file
4. mdrun -rerun on the frame
5. Loop back to step 3 for all frames



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


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