Re: alchemical FEP question

Date: Sat Dec 20 2008 - 05:23:16 CST

Hi Nandhini,

what you are proposing to do is a single-topology transformation, wherein only
the electrostatic component of your potential energy function is altered.

In Namd, the paradigm chosen for alchemical transformations is dual-topology,
where the topologies of both the reference and the target states coexist.

Though you could cook up a quick-and-dirty script that would do the trick and
pretend that Namd handles a single topology, I would advocate that you stick
to the dual-topology paradigm, branching out your molecule into two topologies
where the charge distribution starts to differ (consider the charge distribution
of the initial and the final states).


Selon Nandhini Sokkalingam <>:

> Hello all,
> I am trying to mutate an aromatic compound to another one. The charges on the
> atomic sites for the initial and the target molecule are different while some
> of the
> sites have similar vdw parameters. can i fix the positions of the specific
> atoms with
> similar vdw parameters to account for only electrostatic perturbation and not
> for
> the non-bonded perturbation like in the charging of the sodium atom
> alchemical
> FEP tutorial.
> Thanks
> Nandhini

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:21:36 CST