Dear ambers,
I solved the problem asker later,
Employing a set of files I succeeded to REMD.
MD input or group file could be wrong.
However, I cannot identify the exact reason.
Still, I'd appreciate if you give some advice as for
Similar case.
Best regards,
IK
> -----Original Message-----
> From: kurisaki [mailto:kurisaki.ncube.human.nagoya-u.ac.jp]
> Sent: Tuesday, July 21, 2015 8:17 PM
> To: 'AMBER Mailing List'
> Subject: [AMBER] "nstlim" is not reflected correctly in REMD with pmemd.MPI
>
> Dear Amber developers and users,
>
> I'm trying REMD with Amber14's pmemd.MPI.
> Although REMD simulation proceeds,
> I encountered anomalous situation.
>
> "nstlim" is not reflected correctly,
> Instead, "anomalously huge number" was given for "Total steps" in mdinfo.
>
> Here is one of input files:
>
> =====================================================
> REMD
> &cntrl
> irest=0, ntx=1,
> nstlim=500000, dt=0.002,
> irest=0, ntt=3, gamma_ln=1.0,
> temp0=360.0, ig=21016,
> ntc=2, ntf=2, nscm=1000,
> ntb=0, igb=5,
> cut=999.0, rgbmax=999.0, extdiel = 78.5,
> ntpr=500, ntwx=500, ntwr=100000,
> numexchg=50000,
> /
> ======================================================
>
> I used following command to submit job:
> mpirun -np 24 pmemd.MPI -ng 12 -groupfile remd.groupfile < /dev/null
>
>
> Shown below is mdinfo in the middle of simulation.
> NSTLIM is over 500000 already.
>
> ======================================================
>
> NSTEP = 746000 TIME(PS) = 1492.000 TEMP(K) = 551.07 PRESS = 0.0
> Etot = -395.2254 EKtot = 125.3866 EPtot = -520.6120
> BOND = 18.2740 ANGLE = 77.7230 DIHED = 32.1195
> 1-4 NB = 17.8187 1-4 EEL = -1168.7411 VDWAALS = -7.6935
> EELEC = 590.2709 EGB = -80.3836 RESTRAINT = 0.0000
> TEMP0 = 540.0000 REPNUM = 8 EXCHANGE# = 2
> ------------------------------------------------------------------------------
> | Current Timing Info
> | -------------------
> | Total steps : ********* | Completed : 746000 | Remaining : *********
> |
> | Average timings for last 96000 steps:
> | Elapsed(s) = 59.93 Per Step(ms) = 0.62
> | ns/day = 276.79 seconds/ns = 312.15
> |
> | Average timings for all steps:
> | Elapsed(s) = 479.61 Per Step(ms) = 0.64
> | ns/day = 268.78 seconds/ns = 321.46
> |
> |
> | Estimated time remaining: -495397.8 seconds.
> ------------------------------------------------------------------------------
>
> =========================================================
>
> Maybe, this simulation takes 6 days in my platform.
>
> Why does this kind of error appear?
> Is this due to input file or Amber14 itself?
>
> I'm most grateful if you give some advices to resolve this problem.
>
> Best regards,
>
> Ikuo KURISAKI
>
>
>
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Received on Tue Jul 21 2015 - 06:00:03 PDT
