[gmx-developers] electrostatic potential on atoms
jmaddox at uci.edu
Thu Jan 27 02:55:25 CET 2005
I am attempting to modify GMX to incorporate the redistribution of
atomic charges within a rigid polarizable solute. My general strategy
is to calculate charge fluctuations at each MD time-step with a code
that has been grafted onto the GMX source tree. Then update the charges
in the topology structure: top.atoms.atom[i].q=qnew and have GMX use
these new charges to compute the intermolecular interactions and forces
as usual, step forward in time, and repeat.
The molecular dynamics input to this code is the electrostatic potential
at the positions of atoms whose charges are allowed to fluctuate. This
information is combined with a (sub)set of transition density matrices
that have been tabulated from the results of a previous (external) TDDFT
calculation on the solute.
I have some, albeit very limited, experience adding files to GMX and
using the GMX data structures to parse out and change the topology of
tagged atoms. However, I am not sure what the best way is to go about
extracting the electrostatic potential at these atomic positions.
More information about the gromacs.org_gmx-developers