Hello Dear Amber users
I am sending my question
for the second time since I think at the first time you may have received it
incomplete.
I am simulating a
polymeric system with nearly 80000 atoms including water molecules in a
truncated octahedron box. I am using GPU in the stage of production for
calculations on amber 12 with a GTX680-4G card. I passed the minimization
stages and heating using sander and a 50ps MD for density equilibration using
pmemd.cuda with success. In the stage of production, using pmemd.cuda,
unfortunately after around 29ns, the restart file became full of NaN and the
density of the system became 0.02 and I observed *********** in front of EPtot
and BOND in .out file. Below, you can see the last correct printed set of data
and the first wrong set of data after it in .out file.
check COM velocity,
temp: 0.000006 0.00(Removed)
NSTEP = 14520000 TIME(PS) = 29110.000 TEMP(K) = 298.76 PRESS = -2.3
Etot = -213023.2511 EKtot = 54045.7891 EPtot = -267069.0401
BOND = 1115.0696 ANGLE = 3124.8871 DIHED = 2998.5910
1-4 NB = 1197.1686 1-4 EEL = 19090.5388 VDWAALS = 36880.7209
EELEC = -331476.0160 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 25231.4726 VIRIAL = 25275.4938 VOLUME = 899267.3816
Density = 1.0069
------------------------------------------------------------------------------
check COM velocity,
temp: NaN NaN(Removed)
NSTEP = 14521000 TIME(PS) = 29112.000 TEMP(K) = NaN PRESS = 13836.9
Etot = NaN EKtot = NaN EPtot = **************
BOND =
************** ANGLE = 768366.9708 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = -28.9466
EELEC = -1536273.9759 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 12582912.0000 VIRIAL = 87.0496 VOLUME = 42117284.9745
Density = 0.0215
------------------------------------------------------------------------------
The control file is as
follows:
&cntrl
imin = 0,
irest = 1,
ntx = 5,
ntb = 2, pres0 = 1.0, ntp = 1, taup = 1.0,
cut = 10, ioutfm = 1,
ntr = 0,
ntc = 2,
ntf = 2,
tempi = 300.0,
temp0 = 300.0,
ntt = 1,
tautp = 1.0,
nstlim = 100000000, dt = 0.002,
ntpr = 1000, ntwx = 1000, ntwr = 10000
/
Once again I performed the
simulation but this time saved the rst file in another directory before the
problem happens and performed another simulation using this rst file. This time
again the same problem happened after around 7 ns. Again I repeated this simulation
and saved the rst in another directory before the problem happens and performed
a new simulation using this new rst. This time the same problem happened after
around 4ns. I searched the amber mailing list for the answer of this problem
and observed there were others who encountered this problem while simulating
using GPU. Although it seems unfortunately they did not receive any particular
answer to lead to salvation of their problem, i am still hopeful one can solve
this problem.
Thanks in advance
Mohamad Mahmoudzadeh
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Received on Tue Sep 03 2013 - 05:30:04 PDT
