Hello Ross,
I ran the with pmemd.cuda and found it printing correctly.
So the problem lies somwhere in pmemd.cuda.MPI.
Thanks for the help.
On Tue, Mar 31, 2015 at 11:36 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> 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*
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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>
--
*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 - 21:00:07 PDT
