[gmx-users] g_enemat error

Anton Feenstra feenstra at chem.vu.nl
Mon Feb 10 08:27:02 CET 2003

Ghermes Chilov wrote:
> Hi, Hugo,
> Not long ago I've faced the same problem with g_enemat. In fact I was
> not lucky enough to solve it completely, but I've mentioned that changing
> options in .mdp could have an impact on g_enemat performance: rlist,
> nstlist, pbc and so on. At the end .edr file had all the components I
> suspected but g_enemat could not see them. In this situation gmx-users
> haven't gave me an advise, but I suspect that (if there is no bug in
> the program) only one specific combination of parameters in .mdp works
> while the others - don't. So if you read the manual very carefully,
> probably, you'll be lucky to launch g_enemat.

g_enemat was a hack (by me) to allow to build a matrix of energies, e.g.
all interaction energies between separate residues in a protein. It makes
some hard-coded simple-minded assumptions on how energy groups are named
in the energy file. This might have changed since the time I wrote g_enemat.
(I know David and Erik have been very busy with energies - mainly due to
PME stuff.)
If the names have changed, g_enemat's assumptions don't hold and it will
fail, probably in a very horrible way. I don't have the time at the moment
to look into it, and suspect I won't in the near future. So, you should
check the sourcecode of the program, see how the names are generated and
how they are compared to the energy groups in the energy file.
There are two components involved in the name generation. First is a
pair of groups, e.g. "Protein" and "DRG", or "Lys247" and "Arg21", giving
name bases like Protein-DRG and Lys247-Arg21. Second are the types of
energy, like LJ, LJ-14, LJ-LR, COUL, COUL-14 and so on. Together these
make the full energy group name, and changes could have been in any and
all of them.

Finally, as to the .mdp files, the only things that really influence the
results for g_enemat are the energy_grps you specify. These must be the
same as you put in your groups.dat file. The other options will determine
which energy types there might be, e.g. by changing rcoul and rlist, you
can eliminate COUL-LR.

Finally finally, g_enemat was a hack. It can and should be done in a much
better way. groups.dat should be obsolete, as it is possible to deduce the
relevant names from the energy file itself. But, as I said before, I
don't have the time now, and won't have anytime soon. Also, I don't have
any particular application now for the program ;-{


  ________ ___________________________________________________________
|        | 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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