On Mon, 27 Apr 2015 09:05:05 -0400 Justin Lemkul <jalem...@vt.edu> wrote:
> > > On 4/27/15 9:02 AM, Hannes Loeffler wrote: > > On Mon, 27 Apr 2015 07:43:51 -0400 > > Justin Lemkul <jalem...@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 Cheers, Hannes. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.