[gmx-users] g_enemat problems... again and again

[Anton Feenstra]

Ghermes Chilov wrote:
> 
> >> unfortunately, my appeal concerning troubles with g_enemat has bean
> >> lost in new year holidays, so i sincerely hope that now you could help
> >> me! What's happend:
> 
> KAF> What do you have in your groups.dat file?
> KAF> What energy groups did you select in your .mdp file?
> 
>    In .mdp file i define the following
>     energygrps = Protein Ligand Sol Liquid
> 
>     exlusion groups = protein protein  protein sol  sol sol
> 
>   In .dat file i define
> 
>     3
>     Protein
>     Ligand
>     Liquid
> 
>   I do not search for interactions with frozen water - does it make
>   sense to g_enemat?

Well, with 3 groups, you will get only a matrix of 3x3 = 9 elements,
of which only 6 are unique, and the 3 on the diagonal are probably
not interesting (i.e. protein-protein, which is excluded, ligand-ligand,
which probably is zero, and liquid-liquid). That leaves only three.
Those you can also analyze with g_energy.

The original reason for having g_enemat was to analyse interaction
energies between a large number of groups, i.e. all aminoacids in
a protein. Then it makes sense to show them together in one matrix.


-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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