Re: alchemical FEP question

From: seleg25_at_rsvs.ulaval.ca
Date: Sun Dec 21 2008 - 12:14:41 CST

Hi Christophe and Namd users,

I am interested in that script that would make Namd pretend it do single
topology (without fixing atoms). I am working on one but if there is already one
somewhere I would like to see it.
Are there any plans of implementing single topology in Namd?

Thank you

Sbastien Lgar
Ph. D. Student
Laval University, Quebec

Selon Christophe.Chipot_at_edam.uhp-nancy.fr:

> 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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