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

Ghermes Chilov Ghermes at belozersky.msu.ru
Tue Jan 7 13:19:02 CET 2003

>> 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?

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

Dear Anton,

Of course it is possible to extract several energy components with
g_energy, however the test case i've given below was just to see how
g_enemat works. The next step would be to divide protein surface into
a number of patterns - attractors on MD trajectory and to calculate in
detail energetics of ligand interaction with these sites. And g_enemat
would be very useful in that case ;-)

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

That is! However the number of energy groups allowed (256) is smaller
than typical length of the protein and in case you have too many
energy groups multiple reruns with energy recalculation are
necessary. And if the original reason was to calculate interactions
between aminoacids in the protein, the input file defining the matrix
(not necessarily squair) of groups between which the interaction should
be concerned shoud be read separatly (as .ndx) but not directly as a
long-long string in .mdp file. The same is relevant for every other
field in .mdp where a big number of groups (freeze, exclusion and so
on) are enumerated. Could this information be read from a special
(new) file type?

and at the end, what should i do with my g_enemat? :-)

Best regards,
 Ghermes                            mailto:Ghermes at belozersky.msu.ru

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