[AMBER] NaN problem with GTX680

From: JAVAD MAHMOUDZADEH <mohamad_mahmoudzadeh.yahoo.com>
Date: Tue, 3 Sep 2013 00:12:05 -0700 (PDT)

Hello Dear Amber users
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 new rst file. This time
again the same problem happened but after around 7 ns. Again I repeated this simulation
and saved the new 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 - 00:30:02 PDT
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