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 <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
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--
========================================
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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