feenstra at chem.vu.nl
Wed Sep 1 17:17:41 CEST 2004
Prasad Gajula wrote:
> Dear Gromacs users,
> Can someone suggests me a way to calculate energies (LJ and total energy )
> for each residue individually after MD simulation.
Residues don't have energies. You can calculate the sum of atom-atom interaction
energies within a residue, and of the residue with the rest of the system.
You can define individual residues in an .ndx file, list them under energy_grps
in your .mdp file and use mdrun -rerun to re-calculate energies from a
trajectory. Be aware that there is a limit (about 200) to the number of
energy_groups, so you may have to take a few series of residues at a time.
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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