FEP - Dynamic charges

From: John Baker (pcxjb3_at_nottingham.ac.uk)
Date: Tue May 15 2012 - 12:38:59 CDT

Hi NAMD Users/Developers,

I have been using CHARMM to investigate single-site dual-topology FEP
simulations of mutating methane --> monofluoromethane.

The charge on the central carbon changes as lambda progresses, due to
the fluorine being expressed.

Is it possible to have dynamic charges on certain atoms?

CHARMM has the 'COLO' feature which does this, but I would much prefer
to use NAMD (much faster computation).

If anyone knows how to do this or knows which part of the source code I
need to change/add to, I would be very grateful.

Many Thanks,
John Baker

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