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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>
> --
> 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 - 09:00:07 PST
