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

Sonia Aguilera sm.aguilera37 at uniandes.edu.co
Fri Oct 5 23:19:22 CEST 2012

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

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