did your amber build pass the parallel tests? this is worrisome.
On Wed, Dec 8, 2010 at 11:44 AM, Janzsó Gábor <janzso.brc.hu> wrote:
> Hi Everyone,
>
> So finally it looks like I've found the solution for my problem. It
> had something to do with the parallel environment. The sysadmin
> created a p.e. to utilize better that cluster. The cluster is built
> from 4 core amd processors and that particular p.e. would assign the
> jobs in a manner that the threads of one job wouldn't run on different
> machines instead of the four core of one cpu. Since I used a 64 core
> job (2 core for each of the 32 replicas), the p.e. accepted it (since
> it can be divided by 4) but during the exchanges something got messed
> up. I changed the input so one replica would run on one core, and the
> issue of the temperatures racing up never emerged again.
>
> So the problem wasn't with the input or the parameters, which now seem
> to be alright, since the replicas exchange in the expected fashion. It
> was some kind of informatics-related issue, maybe it is a sign of a
> hidden bug, but only the amber experts could tell that.
> Anyways, I just wrote this so this thread would have some conclusion
> for someone browsing the archives with the same problem.
>
> Take care,
>
> Gabor Janzso
>
>
> Quoting "Adrian Roitberg" <roitberg.qtp.ufl.edu>:
>
> > Dear Gabor
> >
> > Have you tried plotting the distribution of potential energies for the
> > replicas, before they blow up ? They should be basically identical to
> > the ones you get from the individual MD runs.
> >
> > Adrian
> >
> >
> > On 11/30/10 2:59 PM, Carlos Simmerling wrote:
> >> using the same structures at the start can be dangerous since they are
> not
> >> equilibrated at the right T.
> >> this can cause weird things in exchanges. i suggest using the restart
> files
> >> from the runs you just described and initiating remd from that.
> >> On Mon, Nov 29, 2010 at 2:19 PM, Janzsó Gábor<janzso.brc.hu> wrote:
> >>
> >>> Dear Dr. Simmerling,
> >>>
> >>> The replicas have the same input coordinate file, namely the restart
> file
> >>> from the NPT run I used for relaxing the system. So there is no way the
> box
> >>> sizes could be different.
> >>>
> >>> Following your advice, I've run a 5 ns md simulation at each
> temperature,
> >>> and all of the simulations finished correctly. I have created the
> energy
> >>> distribution histogram of each run as you suggested, and there is
> >>> sufficient
> >>> overlap between the potential energies (as far as I can tell). I have
> >>> enclosed an image of the histograms.
> >>> Since the md runs never crashed, I think the problem would be something
> >>> regarding the replica exchange step.
> >>> Any advice what should be the next thing I look into?
> >>>
> >>> Thank you in forward,
> >>>
> >>>
> >>> Gabor Janzso
> >>>
> >>> Quoting "Carlos Simmerling"<carlos.simmerling.gmail.com>:
> >>>
> >>> it's still unclear to me if the initial structures have different
> volumes
> >>>> or
> >>>> not- if yes, this can make exchanges very difficult.
> >>>>
> >>>>
> >>>> I suggest running the identical simulation without remd- meaning set
> up
> >>>> all
> >>>> of the repliacs and temepratures, but do not use remd. check to make
> sure
> >>>> it
> >>>> is still stable (and verify that REMD is the problem). from this,
> extract
> >>>> potential energies from the output files and histogram all of them to
> >>>> ensure
> >>>> that there is overlap between neighbors.
> >>>>
> >>>>
> >>>> On Tue, Nov 23, 2010 at 1:07 PM, Janzsó Gábor<janzso.brc.hu> wrote:
> >>>>
> >>>> Dear Mr. Simmerling,
> >>>>>
> >>>>> I am sorry if I wasn't clear, my goal is to run an NVT study. The NPT
> >>>>> part was only to relax the system after solvating the peptide in the
> >>>>> TFE, just as the tutorials and the manual suggest.
> >>>>>
> >>>>> Regarding your second advice, I am not sure how to create the
> >>>>> histogram of the potential energies if the replicas do not behave as
> >>>>> expected? Should I run simple md runs at each temperature instead?
> How
> >>>>> long such a run shoul be?
> >>>>>
> >>>>> I am also almost sure that the phase transition is not the cause of
> my
> >>>>> problem, since I also tried to run my simulation between 300K and
> 350K
> >>>>> (with 32 replicas), and 350K is just below the boiling point of TFE.
> >>>>> My first guess was the replicas were too far away from each other,
> and
> >>>>> because I have only limited computational capacity at my disposal, my
> >>>>> only option was for sampling the temperatures more frequently,
> >>>>> decreasing the temperature range. Regardless, on lower temperatures,
> >>>>> with smaller deltaT values, the same behavior was observed.
> >>>>>
> >>>>> best regards,
> >>>>>
> >>>>> Gabor Janzso
> >>>>>
> >>>>>
> >>>>> Quoting "Carlos Simmerling"<carlos.simmerling.gmail.com>:
> >>>>>
> >>>>>> it's very important to study REMD examples in the literature before
> >>>>> trying
> >>>>>> something very complex like what you want. First, most studies are
> done
> >>>>> at
> >>>>>> NVT. Check work by Angel Garcia if you want to include pressure
> >>>>> effects.
> >>>>>> Second, it is important to carefully histogram your potential
> energies
> >>>>> for
> >>>>>> the replicas. Like you are trying to sample across a phase
> transition,
> >>>>> which
> >>>>>> is quite challenging. Almost certainly this was not included in your
> >>>>> method
> >>>>>> for selecting the replica temperatures (which you have not told us
> >>>>> about).
> >>>>>>
> >>>>>> perhaps there is something else going on- but I think the first step
> is
> >>>>> to
> >>>>>> try NVT.
> >>>>>>
> >>>>>> 2010/11/23 Janzsó Gábor<janzso.brc.hu>
> >>>>>>
> >>>>>>> Dear Amber Users!
> >>>>>>>
> >>>>>>> I run into a problem with Amber REMD. I am using Amber 9, and I do
> not
> >>>>>>> have the option to upgrade to 11, so any solution working on Amber
> 9
> >>>>>>> would be much appreciated.
> >>>>>>> So, I try to run an NVT simulation of amyloid beta 1-42 (Ab1-42) in
> >>>>>>> explicit TFE solvent.
> >>>>>>>
> >>>>>>> I downloaded the mol2 file I found on REDDB (project code W-16), I
> >>>>>>> used packmol to put 256 molecule into a=30.125 cubic box, and then
> >>>>>>> relaxed the box at 300 K. (first heated up with NVT, than relaxed
> with
> >>>>>>> NPT) I saved the output as a lib file, than used it as the solvent
> box
> >>>>>>> to solve the peptide. I've run some NVT and NPT dynamics to see if
> its
> >>>>>>> stable, and it was, at least up to 400K. At 450K or 500K the
> >>>>>>> simulation stopped, the output said SANDER BOMB stopped the run or
> >>>>>>> something like that. I figured it might be ok, because the boiling
> >>>>>>> point of TFE is at 78°C, and the studies I have found used the
> >>>>>>> temperature range of 300K-400K for TFE solvent simulation.
> >>>>>>>
> >>>>>>> So, I set up a REMD using 32 replicas between 300K and 400K, with
> >>>>>>> Berendsens thermostat (1 ps coupling) SHAKE is on, exchange
> attempts
> >>>>>>> at every 2 ps, and chirality restraints and trans-omega restraints
> are
> >>>>>>> applied.
> >>>>>>> The simulation starts normally, but around the first ten-twenty
> >>>>>>> exchange attempts some replicas heat up like insane. The REMD keeps
> on
> >>>>>>> running, but three replicas are at ~600 000K (!) - and obviously
> they
> >>>>>>> don't participate in the exchanges anymore, so the simulation does
> not
> >>>>>>> stop.
> >>>>>>> The curious thing is, that it always happens after a successful
> >>>>>>> exchange, and it happens always to the same replicas. What I mean,
> in
> >>>>>>> the rem.log file where all the replicas and the relevant info is
> >>>>>>> listed, the 9th, 17th and 25th replicas heat up. Always this three.
> I
> >>>>>>> tried it with different parameters, for example the timestep was
> >>>>>>> reduced to 1 ps, the iwrap option was turned off, the vlimit was
> >>>>>>> reduced to 10, but nothing helped, the same replicas systematically
> >>>>>>> has gone wild every time.
> >>>>>>>
> >>>>>>> If anyone has any idea, what could be the reason for this
> phenomenon,
> >>>>>>> it would be much appreciated.
> >>>>>>>
> >>>>>>> Thanks in advance
> >>>>>>>
> >>>>>>> Gabor P. Janzso
> >>>>>>> PhD student
> >>>>>>> Institute of Biophysics,
> >>>>>>> Biological Research Center
> >>>>>>> H-6726, Szeged, Temesvári krt. 62.
> >>>>>>>
> >>>>>>> Janzsó Gábor Péter
> >>>>>>> PhD hallgató
> >>>>>>> Szegedi Biológiai Központ,
> >>>>>>> Biofizikai Intézet
> >>>>>>> 6726, Szeged, Temesvári krt. 62.
> >>>>>>>
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> >>>>>
> >>>>>
> >>>>>
> >>>>> Gabor P. Janzso
> >>>>> PhD student
> >>>>> Institute of Biophysics,
> >>>>> Biological Research Centre
> >>>>> Hungarian Academy of Sciences Szeged
> >>>>> H-6726, Szeged, Temesvári krt. 62.
> >>>>>
> >>>>> Janzsó Gábor Péter
> >>>>> PhD hallgató
> >>>>> Szegedi Biológiai Központ,
> >>>>> Biofizikai Intézet
> >>>>> 6726, Szeged, Temesvári krt. 62.
> >>>>>
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> >>>>
> >>>
> >>>
> >>> Gabor P. Janzso
> >>> PhD student
> >>> Institute of Biophysics,
> >>> Biological Research Centre
> >>> Hungarian Academy of Sciences Szeged
> >>> H-6726, Szeged, Temesvári krt. 62.
> >>>
> >>> Janzsó Gábor Péter
> >>> PhD hallgató
> >>> Szegedi Biológiai Központ,
> >>> Biofizikai Intézet
> >>> 6726, Szeged, Temesvári krt. 62.
> >>>
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> >> _______________________________________________
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> >>
> >
> > --
> > Dr. Adrian E. Roitberg
> > Associate Professor
> > Quantum Theory Project, Department of Chemistry
> > University of Florida
> >
> > Senior Editor. Journal of Physical Chemistry.
> >
> > on Sabbatical in Barcelona until August 2011.
> > Email roitberg.ufl.edu
> >
> > _______________________________________________
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> >
>
>
>
> Gabor P. Janzso
> PhD student
> Institute of Biophysics,
> Biological Research Centre
> Hungarian Academy of Sciences Szeged
> H-6726, Szeged, Temesvári krt. 62.
>
> Janzsó Gábor Péter
> PhD hallgató
> Szegedi Biológiai Központ,
> Biofizikai Intézet
> 6726, Szeged, Temesvári krt. 62.
>
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Received on Wed Dec 08 2010 - 09:00:09 PST
