[gmx-users] analysis of different groups with g_energy

Mark Abraham 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 
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.


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