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
simulation types.
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.
Mark
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