Re: Soft core potential - tested or not?

From: Chris Chipot (Christophe.Chipot_at_edam.uhp-nancy.fr)
Date: Tue Feb 26 2008 - 15:24:57 CST

Dear Pavel,

to be fair, limitdist is only an ersatz of a true soft-core potential.
It is a temporary workaround, but probably not the safest approach for
tackling end-point catastrophes in a rigorous fashion. The choice of a
single parameter, irrespective of the nature of the atoms at play,
poses under most circumstances obvious difficulties that cannot be
addressed easily.

How can limitdist be tested? I would suggest that you run a toy system
for which you know the answer beforehand. Such is the case for instance
of the zero-sum transformation proposed in the FEP tutorial available
on the NAMD web page.

Since you appear to be in a hurry to publish your data, this info is
probably of lesser importance. Yet, a version of the FEP code featuring
a soft-core potential is currently being implemented and tested, but it
will require additional time before it is ready for production and
distributed.

Chris

Pawel Weronski a écrit :
> Dear FEP experts,
>
> I have conducted a few FEP simulations using NAMD 2.6 with the limitdist
> option. According to the description of this option in the user guide:
> "The potential for atoms closer than limitdist is instead treated as
> a*r^2 + c with parameters chosen to match the force and potential at
> limitdist."
>
> My question is following: has this form of potential been tested or
> validated anyhow? I could find in the literature several other soft core
> potentials but no reports on this particular one. If indeed no reports
> have been published so far, can anybody suggest a simple way to do it? I
> have basically finished the main part of my simulations and would like
> to published the results asap, so I don't want to conduct extensive runs
> anymore. I'll appreciate any suggestions.
>
> Best,
>
> Pawel

_______________________________________________________________________

Chris Chipot, Ph.D.
Equipe de dynamique des assemblages membranaires
Unité mixte de recherche CNRS/UHP No 7565
Nancy Université Phone: +33 (0)3-83-68-40-97
B.P. 239 Fax: +33 (0)3-83-68-43-87
54506 Vandœuvre-lès-Nancy Cedex

                             E-mail: Christophe.Chipot_at_edam.uhp-nancy.fr
                                            http://www.edam.uhp-nancy.fr

     Science without management is worse than management without science

                                                        N. G. van Kampen
_______________________________________________________________________

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