Have you watched your trajectory in 3D?
That might provide a clue.
Bill
<div>-------- Original message --------</div><div>From: Himanshu Joshi <himanshuphy87.gmail.com> </div><div>Date:03/31/2015 10:58 AM (GMT-08:00) </div><div>To: AMBER Mailing List <amber.ambermd.org> </div><div>Subject: [AMBER] AMBER14 pmemd.cuda.MPI : *** in mdout files </div><div>
</div>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 - 18:30:02 PDT
