Dear Sir,
Thank you for the reply
I will try softcore with restraints
Muthukumaran Rajagopalan
On Thu, Feb 1, 2018 at 5:55 PM, David A Case <david.case.rutgers.edu> wrote:
> On Wed, Jan 31, 2018, Muthukumaran Rajagopalan wrote:
> >
> >
> > I am performing thermodynamic integration for the disappearing of few
> > ions in protein complex.
>
> > I am using Sander to convert an ion (initial state) to a dummy atom
> > (final state).
>
> This sounds like something for which you should use softcore: we've tried
> for
> a long time to avoid using dummy atoms. Think of it this way: rather than
> "disappearing" the ions, you rather want to "decouple" the ions: the ions
> are
> still there (no dummy atoms), but in the final state they no longer
> interact
> with their environment.
>
> > I am modifying both the charge and vdw parameters at the same time to
> > make the ion disappear.
>
> This is dangerous without using softcore.
>
> >
> > I am following the tutorial in the below link as a starting point.
>
> www.rosswalker.co.uk/tutorials/psc_workshop/Tutorial_seven/
>
> Sigh...proves you can never escape your past in the modern era. I prepared
> that tutorial, but note the date at the top says "2005", and the example
> files were run in October of 2002. Since then we have learned that
> divergences in "simple" TI when particles disappear are better handled by
> using softcore than by the "klambda" approach. I think this is especially
> true when trying to remove charge and vdw at the same time.
>
> However, I don't think you have been wasting your time, since you have
> clearly
> learned a lot about the innards of what is going on with free energy
> calculations. Your questions are good ones, but I think the only good
> answer
> is to move to an alternate approach.
>
> ...good luck....dac
>
> [For the greybeards on the list: at the tutorial notes, the point of these
> calculations was to demonstate (mainly to myself!) the extent to which
> Amber
> could reproduce the early "extremely precise" free energy results reported
> by
> Michael Shirts. The web page cited above is also on the ambermd.org
> site, but
> with a "deprecated" title, and an introduction explaining that it is
> outdated.
> But I think it is still a good educational exercise, prompting people to
> look
> carefully at how dV/dlambda changes with lambda, and what the problems are
> at
> endpoints -- problems that led most in the field to move towards soft-core
> approaches, as discusse above.]
>
>
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Received on Thu Feb 01 2018 - 21:00:02 PST
