[gmx-users] Gromacs on the HorseShoe

Dr. Vitaly Chaban vvchaban at gmail.com
Thu Jan 10 14:06:19 CET 2013

Morten -

Here is the link to GROMACS 4.5.5, installed on the HorseShoe 6
cluster: /usr/local2/all/gromacs/gromacs-hs6-4.5.5

I suggest you to start with something very simple, such as small
liquid water system. Here it is:

The faster you start with *real systems*, the more meaningful your
research project will seem to you. For instance, try to calculate
radial distribution functions (g_rdf utility in gromacs), diffusion
constant (g_msd utility), density (g_energy utility), viscosity
(g_energy), vaporization enthalpy, etc.

Change temperature (grompp.mdp file), change pressure (grompp.mdp
file) and recalculate the properties.

Change parameters (topol.top file), e.g. H-O-H angle and find our how
this *unreal new water* behaves.

Change the number of molecules (conf.gro) per unit cell and the shape
the box, and observe how this influences water's properties.

Dr. Vitaly V. Chaban
MEMPHYS - Center for Biomembrane Physics
Department of Physics, Chemistry and Pharmacy
University of Southern Denmark
Campusvej 55, 5230 Odense M, Denmark

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