[gmx-users] decomposing forces

David L. Bostick dbostick at physics.unc.edu
Wed Jan 15 16:28:20 CET 2003

Hello all,

I have a system with protein, lipid, water, and an ion.  If I want to find
the different contributions to the force experienced by the ion (i.e.
force due to water on the ion, force due to protein on the ion, etc.), how
might I do this?  My idea is as follows:

1) Run normal MD
2) mdrun -rerun with energy exclusions so as not to calculate interaction
with certain groups

My question is, "will the trajectory file have only the forces not excluded
in the energy group exclusions?"  For example, if I use

energygrp_excl = ion lipid ion protein

and then use mdrun -rerun , will the only force on the ion appearing in the
trajectory file be due to the ion - water nonbonded interaction?

Thanks in advance,

David Bostick					Office: 262 Venable Hall
Dept. of Physics and Astronomy			Phone:  (919)962-0165
Program in Molecular and Cellular Biophysics
UNC-Chapel Hill
CB #3255 Phillips Hall				dbostick at physics.unc.edu
Chapel Hill, NC 27599	           		http://www.unc.edu/~dbostick

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