[gmx-users] energies

[Anton Feenstra]

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.



-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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