[gmx-users] Re: Error There is no domain decomposition for 6 nodes that is compatible
jalemkul at vt.edu
Sat Oct 6 16:35:27 CEST 2012
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
> -------- Original-Nachricht --------
>> Datum: Fri, 05 Oct 2012 23:05:33 -0400
>> Von: Justin Lemkul <jalemkul at vt.edu>
>> An: Discussion list for GROMACS users <gmx-users at 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
>>> useful for partitioning free-energies of relatively large molecules,
>>> 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
>> 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
>> 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
>> are not coupling intramolecular interactions, you may get unnaturally
>> 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 A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> gmx-users mailing list gmx-users at gromacs.org
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Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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