[gmx-users] difference of calculation time between the numbers of fep-lambdas values

Justin Lemkul jalemkul at vt.edu
Mon Apr 27 15:05:19 CEST 2015

On 4/27/15 9:02 AM, Hannes Loeffler wrote:
> On Mon, 27 Apr 2015 07:43:51 -0400
> Justin Lemkul <jalemkul at vt.edu> wrote:
>> Note that without couple-moltype, you're going to be decoupling the
>> whole system, which is (1) not what you want for calculating
>> solvation free energy and (2) extremely slow.  There is an inherent
>> slowdown when running the free energy code, but it should not be so
>> large.
> Really? I just looked into the code yesterday and I think that if you do
> not set couple-moltype, none of the coupling code is ever triggered.  I
> have only played a bit with relative free energies (Gromacs 4.6) where I
> think you don't need any of the couple- parameters at all.

Maybe I got that backwards.  For relative free energies, this is true (we're 
doing these now); topological differences are all that are needed.  For an 
absolute solvation free energy, one needs couple-moltype unless the B-state 
(dummy) is explicitly defined in the topology, AFAIK.  If there is no 
couple-moltype, and no B-state defined in the topology, I'm not sure what the 
code would even be doing, actually.



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


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