[gmx-users] Editing index.ndx, Ener. Groups and rerun

[Erik Lindahl]

Alan Wilter Sousa da Silva wrote:

>Hi List!
>
>	I have system divided in 4 groups (for temperature and energy):
>protein, ligand, water and ion.  I created a 5th new group protein+ligand
>and defined it in my energy-groups at *.mdp file.  However, when I try to
>run grompp I got a error:
>
>Fatal error: Atom 0 in multiple Energy Mon. groups (16 and 0)
>
>0 for group System and 16 for group PR_LIG
>
>Cannot I monitor such group?  Any help would be very welcome.
>
>  
>

The energy monitoring works by separating the system in groups (i.e. 
every single atom HAS to be in some group.). Then, when we calculate the 
interactions, we keep track of the energy groups of the participating 
atoms, and add the contribution to the right place.

This of course also means that an atom can only belong to a single 
energy group.

It's still easy to solve your problem, though. Assume you have four 
energy groups: Protein, HEME, SOL, IONS. If you want to know the energy 
between Protein+HEME and SOL/ION, just run g_energy and add the energy 
of the combinations Protein-SOL and HEME-SOL (or ION). There's even a 
-sum option that does it for you :-)

Cheers,

Erik