From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Wed May 16 2012 - 03:03:54 CDT
No, you cannot have the charge on a given atom change during the
alchemical transformation. In the dual-topology spirit, you should
define two separate molecules, methane and fluoromethane, and define
one as vanishing and one as appearing. Then, for efficiency, restrain
the common part of both molecules to be superimposed (e.g. using the
colvars to enforce a distance restraint centered at zero between the
two carbon atoms).
On 15 May 2012 19:38, John Baker <pcxjb3_at_nottingham.ac.uk> wrote:
> 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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