[gmx-users] Calculating intermolecular energies of water

Justin Lemkul jalemkul at vt.edu
Wed Oct 29 11:28:15 CET 2014

On 10/28/14 2:26 PM, Jackson Chief Elk wrote:
> I am writing a routine in C, to calculate the energy of intermolecular interactions of water in a nano cavity, at each time step.  There is variable number of waters per each simulation step.  I am using the system() function, to repeat the following calls to gromacs over and over.
> 1) g_select (To make an index file of waters at time step i)
> 2) trjconv (To get positions of water at time step i)
> 3) tpbconv (To make *.tpr file for pore water at time step i)
> 4) mdrun -rerun (To get *.edr file)
> 5) g_energy (To calculate short range LJ and Coulomb interaction)
> Would this give me intermolecular interaction energies without having to make a group in an *.mdp file?  Or am I going to have perform grompp instead of tpbconv?

Provided that your topology for water specifies a rigid model, then the 
potential energy of that subset should contain only nonbonded contributions. 
Even if the water isn't rigid, you can still calculate the nonbonded 
contribution from the appropriate energy terms.


> On Oct 28, 2014, at 11:27 AM, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>> On 2014-10-28 18:12, Jackson Chief Elk wrote:
>>> Hi,
>>> When using g_energy to calculate short-range Coulomb interactions between a dynamically sized group of water, made with g_select, does the output contain both bonded and non bonded contributions?
>>> Jackson
>> I don't think this is possible at all. You need to define energy groups before your simulation.
>> --
>> David van der Spoel, Ph.D., Professor of Biology
>> Dept. of Cell & Molec. Biol., Uppsala University.
>> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
>> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
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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


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