[gmx-users] Calculate a single hydrogen bond energy in the polypeptide molecule
feenstra at chem.vu.nl
Tue Aug 10 17:39:14 CEST 2004
Sekwan Oh wrote:
> Dear gmx-users,
> I'm wondering if we can obtain hydrogen bond energy (e.g. N-H ----- O=C)
> in the polypeptide molecule (which is defined as 1 group of residues e.g
> I think I can get the bonded and nonbonded energy of the 1 residue of
> the polypeptide (by using g_energy and setting up 'energygrp' command in
> .mdp file)
> , however I haven't found out a way to get the energy between atoms
> which belong to same group of residues.
You can, if you make your own .mdp file in which you define two groups,
one corresponding to your N-H of interest, and the other to your O=C.
Assuming you name these groups, e.g., 'N-H' and 'O=C', your .ndx file
could look like:
1 2 3 ...
4513 4514 ...
And your .mdp file will contain:
energy_grps = N-H O=C
Using g_energy (after the simulation or the rerun), you can find the
N-H-O=C groups to analyze.
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |
| | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/ |
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