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

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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