[gmx-users] Individual energies of amino acids

[Mark Abraham]

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