Hi Joshi,
If you run with just pmemd.cuda instead of cuda.MPI do you see different behavior?
All the best
Ross
> On Mar 31, 2015, at 10:58 AM, Himanshu Joshi <himanshuphy87.gmail.com> wrote:
>
> Dear Friends,
> I am running pmemd.cuda.MPI (AMBER14) in Tesla K40s gpu cards for an
> explicit water DNA system with SPFP precision model. After running few
> steps sucessfully, I am getting **** for temperature and energy values as
> typed below followed by the md input file.
>
>
> NSTEP = 45000 TIME(PS) = 54230.000 TEMP(K) = 300.15 PRESS =
> 0.0
> Etot = -1102980.4479 EKtot = 216143.9219 EPtot =
> -1319124.3698
> BOND = 8297.0959 ANGLE = 17306.9385 DIHED =
> 22929.3885
> 1-4 NB = 8627.8031 1-4 EEL = -71177.7576 VDWAALS =
> 134764.0741
> EELEC = -1439871.9123 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> ------------------------------------------------------------------------------
>
> check COM velocity, temp: NaN NaN(Removed)
>
> NSTEP = 50000 TIME(PS) = 54240.000 TEMP(K) = NaN PRESS =
> 0.0
> Etot = NaN EKtot = NaN EPtot =
> **************
> BOND = 0.0000 ANGLE = 4770613.6638 DIHED =
> 0.0000
> 1-4 NB = ************** 1-4 EEL = ************** VDWAALS =
> **************
> EELEC = ************** EHBOND = 0.0000 RESTRAINT =
> 0.0000
> ------------------------------------------------------------------------------
> Here is my md input file
>
> Production run with constant volume
> &cntrl
> ntx=6, irest=1,
> nmropt=0,
> ntrx=1, ntxo = 2,
> ntpr=5000, ntwx=5000, ntwr=10000,
> ntwv=0,
> ntf=2, ntb=1,
> cut=9.0, nsnb=10,
> nstlim=1000000, nscm=10000,
> t=0.0, dt=0.002,
> ntt=1, tautp=0.5
> ntp=0, pres0=1.0, taup=0.5, comp=44.6
> tempi=300.0, temp0=300.0,
> ipol=0, ntc=2, ioutfm = 1
> /
> &ewald
> /
>
> Though, I am running another NPT run using Langevin dynamics using
> anisotropic pressure coupling and MC barostate with same pmemd.cuda.MPI and
> it is running fine.
>
> Is it something known problem or I am missing something, please comment.
> Thanks in advance for your valuable time.
>
>
>
>
>
> *With Regards,HIMANSHU JOSHI Graduate Scholar, Center for Condense Matter
> TheoryDepartment of Physics IISc.,Bangalore India 560012*
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Received on Tue Mar 31 2015 - 11:30:02 PDT
