[gmx-users] analysis of different groups with g_energy
Mark.Abraham at anu.edu.au
Tue Jun 10 03:40:57 CEST 2008
Peyman Yamin wrote:
> Hi again,
> Now I remember! some old g_energy let me use numbers as the input for the
> terms I wanted...!
Yeah, it changed going from 3.3 to 3.3.1, IIRC. This allowed for scripts
to be much more general, since the numbers used to change for different
> As you say, it looks like the total energy for different groups is not
> calculated. So I should somehow do it myself? If yes, I don't even know where
> I should get the terms I should add together from? I think I'd need all
> bonding and nonbonding interactions! or I should even calculate them?
See my previous email... the most reliable way is to invoke cpp on your
.top file to do all the #includes, and then to go through it with a text
editor and zero out everything that you feel should be zeroed out.
You'll probably have to halve all of the non-bonded terms yourself by
hand after the mdrun -rerun.
> I can't also find what SR and LR and 14 mean in energy terms...!
short range, long range and 1-4 interactions. See early chapters of
GROMACS manual for details.
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