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

Hannes Loeffler Hannes.Loeffler at stfc.ac.uk
Mon Apr 27 19:14:16 CEST 2015

On Mon, 27 Apr 2015 09:05:05 -0400
Justin Lemkul <jalemkul at vt.edu> wrote:

> 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.

I think it runs a normal MD simulation for each lambda.  A quick test
with a A-state only topology and no couple- parameters gives only
gradients with zero value.  In fact, the output file says

There are 0 atoms and 0 charges for free energy perturbation


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