[gmx-users] Calculating intermolecular water interactions
Jackson Chief Elk
jchiefelk at gmail.com
Tue Oct 21 17:33:02 CEST 2014
Thanks for the direction Justin. I will probably end up writing my own C program that does this, possibly by using the system() function to call on gromacs commands when needed. I'll be sure to put it on Sourceforge when its done.
On Oct 21, 2014, at 6:28 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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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