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
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
