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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Received on Tue Nov 30 2010 - 06:30:06 PST
