Dear Dr. Simmerling,
Yes, the build passed the parallel tests. As far as I know, it is at
least a two year old build, and many parallel simulations were
successfully run on it.
I would try it with 4 core for each replica, but with as many replicas
as I need, the simulation would require more cores than the cluster has.
Gabor Janzso
Quoting "Carlos Simmerling" <carlos.simmerling.gmail.com>:
> 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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>> >>>>>>>
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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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>> >>>>> _______________________________________________
>> >>>> AMBER mailing list
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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
>> >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>>
>> 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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>
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 - 09:00:11 PST
