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

Anton Feenstra feenstra at chem.vu.nl
Tue Jan 7 13:33:58 CET 2003

Ghermes Chilov wrote:
> 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 ;-)

OK! Testing on a simple example is a good thing!

> 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?

In principle, yes. But in practice I don't know. I wouldn't be
particularly happy about adding another input file to mdrun (or
to grompp). It would probably not be too hard to write a script
and/or small program that generates the necessary .mdp file(s)
from a list of groups, and performs the reruns.

Alternatively, one could write a separate program that re-calculates
all interaction energies that you want, possibly including the (very
expensive) Ewald part between sub-sets of the system. That would be
similar to mdrun -rerun, except that you de-couple it completely 
from the md-engine giving you more freedom to choose e.g. flexibility
versus performance.

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

Don't know. The input routines g_enemat uses to parse the energy
file are not very sophisticated. It might simply be that (some of)
the energy groups have been (slightly) re-named since g_enemat
was written (by me, BTW). But IIRC g_enemat specifies which energy
groups it is looking for, and you should be able to check if the
names exactly match those that e.g. g_energy reports.


 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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| ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
|  /  \  |-----------------------------------------------------------|
| (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
|  \__/  | Nijenborgh 4 - 9747 AG Groningen - The Netherlands        |
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|  /  \  | K.A.Feenstra at chem.rug.nl - http://md.chem.rug.nl/~anton   |
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