From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Sun Oct 12 2008 - 19:48:28 CDT
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
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
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> Thanking you,
MS> On Sat, 11 Oct 2008, Chris Harrison wrote:
MS> > Monika,
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> > Chris
-- ======================================================================= Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot.
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