[gmx-users] Re: Error There is no domain decomposition for 6 nodes that is compatible

[lloyd riggs]

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 <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
> 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
> 
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