[gmx-users] Calculating intermolecular energies of water

Jackson Chief Elk jchiefelk at gmail.com
Tue Oct 28 19:26:09 CET 2014

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?

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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