[gmx-developers] electrostatic potential on atoms

Jeremy Maddox jmaddox at uci.edu
Thu Jan 27 02:55:25 CET 2005

Dear GMX-developers,

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.

Any advice?

Thank you,

Jeremy Maddox

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