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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Received on Tue Nov 23 2010 - 10:30:03 PST
