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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Received on Tue Nov 30 2010 - 06:30:04 PST
