[gmx-users] Fwd: Bad performance in free energy calulations

Justin Lemkul jalemkul at vt.edu
Tue May 19 20:49:06 CEST 2015

On 5/19/15 12:12 PM, Hannes Loeffler wrote:
> On Tue, 19 May 2015 12:03:41 -0400
> Michael Shirts <mrshirts at 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 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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


More information about the gromacs.org_gmx-users mailing list