[gmx-users] Re: Energy calculation problem with molecule leaving the box
ghorvat at chem.pmf.hr
Fri Feb 4 14:19:11 CET 2011
I extracted trajectories with -pbc center -mol to obtain ones with
molecules that form different energy groups in all combinations and then
rerunned the simulation. This procedure was described here
I seem to get a reasonable interaction energy throughout the simulation
and no zeroes. Is this a good procedure to calculate interaction energy?
The reason why I am doing energy calculations posteriori is that a
solvent molecule enters the calixarene cavity but I don't know which one
is doing that until after the simulation.
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From: Mark Abraham <Mark.Abraham at anu.edu.au>
Subject: Re: [gmx-users] Energy calculation problem with molecule leaving
Date: Fri, 04 Feb 2011 15:04:54 +1100
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