Hello,
I recently updated an Amber 12 install with the latest bugfixes (#23 for
AmberTools, #9 for Amber). I'm now having problems during minimization for
a protein system in an octahedral TIP3P water box, which is neutralized
with Na+ atoms and has a total of ~139000 atoms. The minimization runs all
1000 steps specified, but the total energy doesn't decrease from the
initial 6.1E+06. In particular, the VdW energy always stays at a very high
value.
I noticed that the RESTRAINT energy is always at 0.0, even though I set a
restraint mask for heavy atoms. This is the mask I used: ' !(:WAT) &
!(:Na+) & !(.H=) '. I know this mask works because I used it in
successfully minimizing another smaller system (~56000 atoms) using the
same Amber 12 setup and control scripts.
Since the setup works for the smaller system but not the larger one, I was
wondering if there has been a reported problem in system size when doing
minimization over the GPU? I'm using CUDA 4.2, and can replicate this
problem on a GTX580 and GTX680.
Thanks,
Tim
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Sep 05 2012 - 09:30:04 PDT
