No, we received the full message the first time (at least I did). I
suggest looking at the advice given in the two responses to your first
question.
All the best,
Jason
On Tue, Sep 3, 2013 at 8:18 AM, JAVAD MAHMOUDZADEH <
mohamad_mahmoudzadeh.yahoo.com> wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Sep 03 2013 - 05:30:06 PDT
