Re: [AMBER] md simulation error

From: Kehinde Idowu <>
Date: Sat, 28 Nov 2020 19:34:22 +0000 (UTC)

 Dear David,
The job fail at the beginning and no output was produced. I ran it with CPU and it works.
This is my file;Equilibration Step of MMP3 (MMMM): stage-1 &cntrl  imin= 0,  iwrap=1,  irest=1,  NTX=5,  ntb=2,  ntp=1,  PRES0=1.0,  TAUP=2.0,  NTPR=500,  NTWX=500,  NTWR=500,  ntr=0,  Tempi=300.0,  Temp0=300.0,  NTT=3,  gamma_ln=1.0,  NTC=2,  NTF=2,  cut=12.0,  nstlim=10000000,  dt=0.002,  ntxo=1,  ioutfm=0, /

    On Saturday, November 28, 2020, 12:14:33 AM GMT+2, David A Case <> wrote:
 On Fri, Nov 27, 2020, Kehinde Idowu wrote:

>Please, I am running an md simulation on GPU but the job is
>terminated giving this error message 'Post job file processing error;
>job3194139.sched01 on host gpu4002' .

>I have checked my md_error file, this is the message I am
>getting 'Note: The following floating-point exceptions are

This is not an error, but a common message.  What kind of output did you
get?  Does it look like things finished normally?  Did it get almost to
the end, and then fail, or fail right at the beginning?  Does a (perhaps
shorter) CPU job with the same input work OK?

Does your script do anything after the Amber run, such as copy/move or
remove files?  It's possible that the "post job file processing error"
has nothing to do with Amber per se.


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Received on Sat Nov 28 2020 - 12:00:02 PST
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