it seems strange that it passes the parallel REMD tests, but fails for your
system. As you say, it indicates a bug in the code but I don't have much
info to try and locate it.
On Wed, Dec 8, 2010 at 11:57 AM, Janzsó Gábor <janzso.brc.hu> wrote:
> 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.
> >> >>>>>>>
> >> >>>>>>> ----------------------------------------------------------------
> >> >>>>>>> This message was sent using IMP, the Internet Messaging Program.
> >> >>>>>>>
> >> >>>>>>>
> >> >>>>>>> _______________________________________________
> >> >>>>>>> AMBER mailing list
> >> >>>>>>> AMBER.ambermd.org
> >> >>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >> >>>>>>>
> >> >>>>>> _______________________________________________
> >> >>>>>> 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.
> >> >>>>>
> >> >>>>> ----------------------------------------------------------------
> >> >>>>> This message was sent using IMP, the Internet Messaging Program.
> >> >>>>>
> >> >>>>>
> >> >>>>> _______________________________________________
> >> >>>>> AMBER mailing list
> >> >>>>> AMBER.ambermd.org
> >> >>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >> >>>>>
> >> >>>>> _______________________________________________
> >> >>>> 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.
> >> >>>
> >> >>> ----------------------------------------------------------------
> >> >>> This message was sent using IMP, the Internet Messaging Program.
> >> >>>
> >> >>> _______________________________________________
> >> >>> AMBER mailing list
> >> >>> AMBER.ambermd.org
> >> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >> >>>
> >> >>>
> >> >> _______________________________________________
> >> >> AMBER mailing list
> >> >> AMBER.ambermd.org
> >> >> http://lists.ambermd.org/mailman/listinfo/amber
> >> >>
> >> >
> >> > --
> >> > 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.
> >>
> >> ----------------------------------------------------------------
> >> This message was sent using IMP, the Internet Messaging Program.
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > _______________________________________________
> > 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.
>
> ----------------------------------------------------------------
> This message was sent using IMP, the Internet Messaging Program.
>
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Dec 09 2010 - 06:00:02 PST
