[gmx-users] using g_enemat

[K.A.Feenstra]

sadhna wrote:
> 
> hi all,
>        I want to calculate VdW interactions between atoms in protein using
> g_enemat option but i am confused about the -groups option.
> Do I have to make an input file with different atoms in different residues
> in pairs so that it would output the interaction energies between atom
> pairs....could any one provide me with the sample of input file for
> -groups option.

There is two things you need:
1) an energy file which already contains energies for all of the groups
you are interested in. For example if you have a Gly-Gly-Gly tripeptide
(silly example), you would make an index file like this (the atom
numbers are bogus in this example):
--index.ndx--
[ Gly1 ]
	0 	1 	2 	3
[ Gly2 ]
	4 	5 	6 	7
[ Gly3 ]
	8 	9 	10	11
--index.ndx--
Then, you must tell mdrun to calculate energies for each of the groups,
by putting in your .mdp file:
energy_groups = Gly1 Gly2 Gly3
If you already performed the simulation, you can re-calculate the
energies by making a new .tpr file with the energy_groups option and
the index file, and using the -rerun option of mdrun.
2) use g_enemat to extract the energies from your energy file and plot
them. Here you need the groups.dat file, which should look like:
--groups.dat
3
Gly1
Gly2
Gly3
--groups.dat--
which will cause g_enemat to produce a 3x3 matrix of interaction energies.


-- 
Groetjes,

Anton
 _____________ _____________________________________________________
|             | Anton Feenstra       Dept. of Biophysical Chemistry |
|  _   _  ___,| K.A.Feenstra at chem.rug.nl    University of Groningen |
| / \ / \'| | | Tel +31 50 363 4327                    Nijenborgh 4 |
|(   |   )| | | Fax +31 50 363 4800               9747 AG Groningen |
| \_/ \_/ | | | http://md.chem.rug.nl/~anton        The Netherlands |
|             | "Ease Myself Into the Body Bag" (P.J. Harvey)       |
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