Re: [gmx-users] Re: Error There is no domain decomposition for 6 nodes that is compatible
On 10/6/12 10:23 AM, lloyd riggs wrote: Could you explain to me how this would effect your domain decomposition? Pairs are two-body interactions. If they are applied to protein atoms that are very far apart (which is not normally the case) then the DD cell sizes get very large. -Justin Original-Nachricht Datum: Fri, 05 Oct 2012 23:05:33 -0400 Von: Justin Lemkul An: Discussion list for GROMACS users 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 listgmx-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 -- 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 listgmx-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
Re: [gmx-users] Re: Error There is no domain decomposition for 6 nodes that is compatible
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 > An: Discussion list for GROMACS users > 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 listgmx-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 listgmx-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
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 listgmx-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] Re: Error There is no domain decomposition for 6 nodes that is compatible
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? Thank you again, Sonia Aguilera Graduate Assistant Universidad de los Andes-Colombia -- View this message in context: http://gromacs.5086.n6.nabble.com/Error-There-is-no-domain-decomposition-for-6-nodes-that-is-compatible-tp5001648p5001707.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-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
