On 5/19/15 12:12 PM, Hannes Loeffler wrote:
On Tue, 19 May 2015 12:03:41 -0400
Michael Shirts <mrshi...@gmail.com> wrote:
Yep, that's what I generally do. Almost all alchemical changes
involve a difference in two calculations (since the alchemical change
itself is unphysical). Even one-calculation solvation free energy
calculations are actually calculating the difference in free energy
from liquid to vapor state.
This reminds me: there was recently a discussion around couple-moltype
on this list. My understanding is that this can be used for "absolute"
free energies. But what I really want to make sure is this: as far as
I can see in the code and I think the manual says that too is that when
couple-moltype is not set in the .mdp none of the other couple-
parameters have any effect should I set any of the to something. Do I
get this right?
Right, they're ignored.
-Justin
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
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http://mackerell.umaryland.edu/~jalemkul
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