Could you explain to me how this would effect your domain decomposition?
-------- Original-Nachricht -------- > Datum: Fri, 05 Oct 2012 23:05:33 -0400 > Von: Justin Lemkul <jalem...@vt.edu> > An: Discussion list for GROMACS users <gmx-users@gromacs.org> > Betreff: Re: [gmx-users] Re: Error There is no domain decomposition for 6 > nodes that is compatible > > > On 10/5/12 5:19 PM, Sonia Aguilera wrote: > > Thank you a lot, > > > > I only changed the couple-intramol setting (couple-intramol=yes) and now > > it´s running just fine. However I have a doubt about something. In the > > manual says the following when using couple-intramol=no > > > > "In this manner the decoupled state of the molecule corresponds to the > > proper vacuum state without periodicity effects" > > > > I don´t understand the real effects and implications of this on my > > simulation. Does it mean that it is better to run with > couple-intramol=no? I > > also read that using couple-intramol=yes has it's advantages: "This can > be > > useful for partitioning free-energies of relatively large molecules, > where > > the intra-molecular non-bonded interactions might lead to kinetically > > trapped vacuum conformations. Again, I don't understand what is the real > > meaning of that. Can you please make this clear for me? > > > > Consider what (de)coupling means. You are manipulating the interactions > of a > chosen molecule with its surroundings as a function of lambda. If you > tell > mdrun that your calculation should not couple intramolecular interactions > (couple-intramol = no) then what that is saying is that all nonbonded > interactions within that given molecule are always calculated at full > strength. > That is what the manual is telling you - the calculation implies that > intramolecular terms are always on, as if the molecule were in a vacuum. > If you > do couple intramolecular interactions (couple-intramol = yes), then any > nonbonded interactions within your molecule of choice are also scaled as a > function of lambda. This may be beneficial for large molecules, since if > you > are not coupling intramolecular interactions, you may get unnaturally > strong > interactions within the solute molecule since the interactions with the > surrounding solvent are weakened as a function of lambda. Thus you can > get odd > geometries that get trapped and are detrimental to your sampling. > > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists