Re: Query Regarding FEP tutorial: NPT or NVT?

From: mon_sharma_at_research.iiit.ac.in
Date: Mon Oct 13 2008 - 01:54:21 CDT

Hi!!

Thank you for the insight. :) I also agree with you, just wanted to clear
my doubts. Thanks a lot.

Regards,
Monika

On Sun, 12 Oct 2008, Axel Kohlmeyer wrote:

> On Sun, 12 Oct 2008, mon_sharma_at_research.iiit.ac.in wrote:
>
> MS> Hi!! It doesnt seem like typo. I mean the paragraph certainly tells you to
> MS> use NPT for solvated system and just constant temperature for in vacou
> MS> simulations. Then the free energy values are obtained and subtracted to
>
> monika,
>
> please note that a lot of the properties that are used to calculate
> thermodynamic properties (e.g., temperature or volume) are ill defined
> for droplet ("in vacuo") systems. the fact that you run in NVT/NVE
> is a technicality.
>
> ignoring all kinds of artefacts that arise from using a droplet, i would
> actually claim that the outcome would be more similar to NPT than to a
> "dense" NVT system.
>
> the key point is that in a constant volume ensemble the system cannot
> perform pressure-volume work, but the volume of the droplet can
> (obviously) change, even if you cannot determine its absolute
> value exactly.
>
> cheers,
> axel.
>
>
> MS> obtain net solvation free energy del (del G) as written in tutorial. As far
> MS> as vacuum simulations are concerned, they are better with NVT and NVE, so
> MS> what should be the right thing to calculate here. and what ensembles need to
> MS> be run with in vacou and solvated.
> MS> I wish to request FEP tutorial persons to please consider this query, so
> MS> that this tutorial can be made more informative for persons like me, who are
> MS> curious to adopt this methodology or will adopt in future. :)
> MS>
> MS> Thanking you,
> MS>
> MS> Regards,
> MS> Monika
> MS> On Sat, 11 Oct 2008, Chris Harrison wrote:
> MS>
> MS> > Monika,
> MS> >
> MS> > I am fairly certain this is a typo. Helmholtz free energies are obtained
> MS> > from isothermal ensembles (NVT). Gibbs free energies are obtained from
> MS> > isothermal, isobaric ensembles (NPT).
> MS> >
> MS> > Chris
> MS> >
> MS> >
> MS> >
>
>

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