Dear Amber users,
I would like to ask you about `MPI Quiescence problem` that I've
encounterd during REMD.
I was trying to two set of REMD's, each of which consists of 64 replicas
for (1) monomer, (2) protein system, respectively using the Amber9 on
the AMD/Suse10.1 cluster.
For the (1) monomer system REMD run, REMD worked well up to
Temp-exchange production run as shown in the attached to this message;
"monomer-REMD.result" and "monomer-REMD-pr-Texchange.out".
In contrast to monomer case, for the (2) dimer system REMD, I performed
additional step -- using the NMR restraint option -- to prevent overflow
of rst's for every 64 targeted Temp elevation and indeed obtained
non-overflow rst files.
Then again, however, dimer-REMD(Temp exchange) doesn't work and the run
ended up with following message:
===
MPIRUN: MPI progress Quiescence Detected.
MPIRUN: 48 out of 64 ranks showed no MPI send or receive progress in 900
seconds.
===
In order to check whether indeed MPI communication problem related to
the cluster system itself or rather relevant to dimer-REMD setup, I ran
"monomer-REMD" again (because it was alreday confirmed that working
well). It turned out that monomer-REMD ran okay as usual, so MPI system
itself is not problematic, but then I have no clue but asking you some
help on this issue.
For more your information, I attached both monomer and dimer REMD result
(showing how temperatures exchanges are performed) and both REMD run's
output message.
Has anyone ever met this kind of problem before? Thanks a lot.
_____________
In-Hee Park
[2007-06-27.Wed.4:14pm] Carlos Simmerling wrote `Re: AMBER: rst overflow...'
I would suggest trying a distance restraint on the center of mass but using
the NMR restraint option and setting the r2 distance short (1A)
and the r3 to be larger, say 100A. That way it can move between these
without any penalty but not move farther than 100A. I have to say, though,
that one the dimer dissociates you will have a hard time getting it back.
I am not aware of any studies using REMD on multiple chains except for
looking at oligomerization of short chains under periodic boundary
conditions.
I would check the literature to see the current state of the art for
figuring out protein-protein interaction- I don't think MD is the way to
go. If you know the interface and just want to optimize it, then using
shorter
distances in the restraint to keep it from dissociating would be better, but
you'll have to go carefully and may have to try many variations to find a
protocol
that works well. It all depends on what you mean by "drastic" changes.
I would consider it an unsolved research problem.
On 6/27/07, In Hee Park <ipark.chemistry.ohio-state.edu> wrote:
>
> Dr. Simmerling,
>
> Thanks for your critical help, your prediction was correct. The dimer
> equilibration to the target Temp ended up with overflowing again even
> with option "NSCM" used.
>
> Could you give me more guidance on your suggestion that setting a
> restraint to keep the centers of mass from getting too far apart? Since
> I am interested in conformational changes around the dimer interface,
> which is at the center of mass, I am a bit hesitating just setting up
> the typical group restraint around that interface.
>
> If as long as I am concerned about getting kind of drastic
> conformational changes on around the interface, then LES of dimer would
> be better?
>
> Thanks for your help.
>
> _____________
> In-Hee Park
>
> [2007-06-26.Tue.11:35am] Carlos Simmerling wrote `Re: AMBER: rst
> overflow...'
>
> with a dimer I am not sure if that is correct if the problem is that the
> CM of the system (the dimer) is still at the origin.
> the monomers may drift far apart. in essence, what you are simulating
> is two monomers at infinite dilution. you probably should set a
> restraint
> to keep the centers of mass from getting too far apart, or write some
> code
> to keep the monomers inside a virtual box.
>
> On 6/26/07, David A. Case <case.scripps.edu> wrote:
> >
> > On Tue, Jun 26, 2007, In Hee Park wrote:
> > >
> > > Although setting "iwrap=1" is recommended to keep the coordinate
> output
> > > from overflowing the trajectory file format, this option can be used
> PME
> > > run only. Now, it just shifting to explicit(or hybrid)-REMD the only
> > > possible way to make my dimer REMD possible? Is there no way to
> resolve
> > > the overflow problem under GB?
> > >
> >
> > I think the nscm option can be used to do what you want for GB runs.
> >
> > ...dac
> >
> >
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>
>
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Received on Wed Jul 11 2007 - 06:07:58 PDT
