There were no errors reported in mdout file. I copy the last lines of the mdout as below:
wrapping first mol.: -66.55658 0.00000 0.00000
NSTEP = 6675000 TIME(PS) = 6815.000 TEMP(K) = 299.11 PRESS = -4.8
Etot = -56626.2450 EKtot = 13964.7065 EPtot = -70590.9515
BOND = 521.0486 ANGLE = 1566.6843 DIHED = 3053.7681
1-4 NB = 602.8847 1-4 EEL = 4857.9304 VDWAALS = 7874.4691
EELEC = -89067.7367 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 5987.8215 VIRIAL = 6011.1862 VOLUME = 226960.9976
Density = 1.0268
Ewald error estimate: 0.7158E-04
------------------------------------------------------------------------------
wrapping first mol.: -66.54550 0.00000 0.00000
-----Original Message-----
From: Jason Swails [mailto:jason.swails.gmail.com]
Sent: Monday, May 05, 2014 10:13 AM
To: amber.ambermd.org
Subject: Re: [AMBER] Extract velocity from the restart file
On Mon, 2014-05-05 at 13:39 +0000, Yin, Guowei wrote:
> Hi Jason,
>
> Thanks for your suggestions. By the way, sometimes, only the sentences
> like below shown in log file without saying Vlimit:
>
> pmemd.MPI 000000000041E2D6 Unknown Unknown Unknown
> libc.so.6 00000030FD01D994 Unknown Unknown Unknown
> pmemd.MPI 000000000041E1D9 Unknown Unknown Unknown
> ----------------------------------------------------------------------
> ---- orterun has exited due to process rank 0 with PID 1984 on node
> n-5-2 exiting without calling "finalize". This may have caused other
> processes in the application to be terminated by signals sent by
> orterun (as reported here).
>
> What would this mean? The run just stopped with not any clear indications. Thank you.
Look in the mdout file -- error messages are often printed there.
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon May 05 2014 - 07:30:03 PDT
