Dear Dr. Hannes,
Thnak you for your suggestion. As per your suggestion, I have tried with
the following command, and got this error message.
*mpirun -np 10 pmemd.MPI -O -i 05_Prod.in -p DOPC_128.prmtop -c
04_Hold_1.rst -r prod.rst -x prd.mdcrd -inf md.mdinfo &*
[1] 127720
amber-dopg-chl> forrtl: severe (19): invalid reference to variable in
NAMELIST input, unit 5, file
amber-dopg-chl/05_Prod.in, line 23, position 10
Image PC Routine Line Source
libintlc.so.5 00002B0941DDAB2D Unknown Unknown Unknown
libintlc.so.5 00002B0941DD9635 Unknown Unknown Unknown
libifcore.so.5 00002B0941480535 Unknown Unknown Unknown
libifcore.so.5 00002B09413F2A2D Unknown Unknown Unknown
libifcore.so.5 00002B09413F21E7 Unknown Unknown Unknown
libifcore.so.5 00002B0941435776 Unknown Unknown Unknown
pmemd.MPI 0000000000501D45 Unknown Unknown Unknown
pmemd.MPI 000000000040F894 Unknown Unknown Unknown
pmemd.MPI 00000000004033B4 Unknown Unknown Unknown
pmemd.MPI 00000000004032BC Unknown Unknown Unknown
libc.so.6 00002B0941F29BC6 Unknown Unknown Unknown
pmemd.MPI 00000000004031B9 Unknown Unknown Unknown
===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= PID 127722 RUNNING AT uv
= EXIT CODE: 19
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
On Tue, Sep 23, 2014 at 5:21 PM, Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk
> wrote:
> -inf requires a file name which in your case is '-r'. This then
> leaves '05_Prod.rst' as the next flag. The usage message told you
> how to run pmemd quite clearly.
>
>
> > *mpirun -n 50 pmemd.MPI -O -i 05_Prod.in -o 05_Prod.out -p
> > DOPC_128.prmtop -c 04_Hold_1.rst -inf -r 05_Prod.rst -x 05_Prod.nc &*
> >
> >
> > The errors were
> >
> > unknown flag: 05_Prod.rst
> >
> > usage: pmemd [-O] -i mdin -o mdout -p prmtop -c inpcrd -r restrt
> > [-ref refc -x mdcrd -v mdvel -e mden -inf mdinfo -l logfile]
> > [-ng numgroups -groupfile groupfile -rem remd_method]
> > [-amd amdlog_name -suffix output_files_suffix]
> --
> Scanned by iCritical.
>
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Received on Tue Sep 23 2014 - 02:00:02 PDT
