Re: alchemical FEP question

From: Christophe.Chipot_at_edam.uhp-nancy.fr
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).

Chris

Selon Nandhini Sokkalingam <at5629_at_wayne.edu>:

> 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
>
>

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