[gmx-users] Individual energies of amino acids
Mark Abraham
Mark.Abraham at anu.edu.au
Fri Jun 8 03:17:40 CEST 2007
abhigna polavarapu wrote:
> Hi Mark,
> I need to calculate the individual energies of aminoacids
> using Gromacs. But while using energygrps option in .mdp file for each
> amino acid I can only calculated the nonbonded energies of this residue.
> Is there a way where I can calculated the bonded interactions for each
> amino acid?
I don't think this is a sensible thing to do within the context of the
molecular mechanics approximation. Anyway, if you can come up with a
sensible partition of the bonded terms (e.g. to which amino acid does a
backbone C-N-C-C dihedral term belong?) then you can invent topology
files that only have that partition, construct run input files with
small cut-offs (since you don't want accurate nonbonded energies here)
and use mdrun -rerun to find the bonded energy of your subset of
interactions, and add them to the corresponding nonbonded energy. The
bonded energies are probably dwarfed anyway.
Mark
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