Dear Amber Users,
I am simulating 4 variations of the protein kinase A (PKA) tetramer using
explicit solvent. One of them has 1 Mg ion between each R-C subunits. First
I did the minimization with 10 kcal/mol restraint weight on the backbone.
Then, when I tried to run the heating simulation, the calculation stopped
at step 0, without leaving any error messages in the output file.
The end of the output file looks like this:
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
-3062.5
Etot = -409445.2805 EKtot = 0.0000 EPtot =
-409445.2805
BOND = 49371.8329 ANGLE = 1469.1848 DIHED =
10100.8048
1-4 NB = 2093.2049 1-4 EEL = 24175.6479 VDWAALS =
97254.9978
EELEC = -593910.9535 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 0.0000 VIRIAL = 70377.8192 VOLUME =
1064336.6826
Density =
0.8515
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
In the log file, I got the message "cudaMemcpy GpuBuffer::Download failed
unspecified launch failure". This problem did not occur when I run the
other 3 variations of PKA structures (one with 2 Mg ions, one with no Mg
ions and one with no ADPs).
I have tried to run the simulation using GTX 680, 690, 780, and on the
Stampede supercomputers that use Tesla K20m, I got the same result.
Then I changed the size of the solvent box (from 12A to 10A), the problem
went away and the calculation completed successfully. However, same problem
happened again in the later NVT equilibration simulation. This time the
calculation stopped in the middle:
NSTEP = 1599000 TIME(PS) = 3598.000 TEMP(K) = 299.24 PRESS =
22.1
Etot = -432512.9372 EKtot = 90851.5391 EPtot =
-523364.4763
BOND = 3740.6596 ANGLE = 10689.2110 DIHED =
21485.9623
1-4 NB = 4601.7696 1-4 EEL = 47865.1134 VDWAALS =
74622.8763
EELEC = -687021.9668 EHBOND = 0.0000 RESTRAINT =
651.8984
EAMBER (non-restraint) = -524016.3746
EKCMT = 38312.0157 VIRIAL = 37612.0350 VOLUME =
1465745.9675
Density =
1.0384
------------------------------------------------------------------------------
Same message in the log file "cudaMemcpy GpuBuffer::Download failed
unspecified launch failure".
When I was simulating 4 variations of the heterodimer of PKA (half size of
the tetramer), same error occurred in the heating stage for the structure
with no Mg ions and the structure with no ADPs, while the ones with 1 Mg
and 2 Mg ions are running just fine. So I changed the size of solvent box
from 10A to 8A and this got rid of the problem again. Now I am running the
NVT equilibration and "expecting" the calculations to stop in the middle
just like what happened to the tetramer with 1 Mg (hopefully not).
I would be really grateful if anyone could give me an idea what is going on
and possibly with a solution to this annoying "cudaMemcpy
GpuBuffer::Download failed unspecified launch failure" problem.
Thank you!
Best,
Richard
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Received on Wed Jul 17 2013 - 14:30:02 PDT
