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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Received on Tue Nov 23 2010 - 07:30:04 PST
