Hi Midhun,
The -A only appends the output files afaik, this has nothing to do with the
simulation restart. The -c flag will try to read coordinates and velocities
from the file if you have the proper input instructions in the "in" file
(irest = 1 and ntx = 5, for example). The restart file will be written
where your -r flag is pointing to every ntwr steps; you can use that file
to restart a simulation if you need to. Please check the manual for more
info.
Cheers,
2018-05-22 7:22 GMT+02:00 Midhun K Madhu <midhunk16.iiserb.ac.in>:
> Hello Stephan,
>
> Does that mean we cannot append the data to the existing files in a normal
> simulation
> after a failure of the complete run
> ? If that is the case, should
> I edit the number of steps in I my
> '
> .mdin
> '
> file also?
>
>
> > Message: 3
> > Date: Sun, 20 May 2018 17:27:10 +0200
> > From:
> >
> > Stephan Schott <schottve.hhu.de>
> > Subject: Re: [AMBER] Restart From Check point File
> > To: AMBER Mailing List <amber.ambermd.org>
> > Message-ID:
> > <CAOBY5rjtbjwYZb69JD8m+=eF8JZJYuBgpDNN-f5yOC1dOiP5LA.mail.
> > gmail.com>
> > Content-Type: text/plain; charset="UTF-8"
> >
> > Hi Midhun,
> > The -A flag is for appending outputs, and as stated in the manual, mainly
> > for replica exchange runs, so this is not what you should look for. For
> > restarting your simulation using the -c flag should be enough, as you
> wrote
> > in the command line you have there ("... -c run-prev.rst ..."). If this
> is
> > the exact line you used before, you should have a run.rst, which can be
> > used to restart your run. Just rename your files appropiatelly, and be
> > aware that the -O flag means that if you use the same filenames, the
> > previous files will be overwritten.
> >
> > Cheers,
> >
> > 2018-05-20 14:47 GMT+02:00 Midhun K Madhu <midhunk16.iiserb.ac.in>:
> >
> > > Hello all,
> > >
> > > While Running pmemd.cuda.MPI I am not able to use -A option which is,
> as
> > > per AMBER16 manual, is the option for appending to the existing output
> > > files. It says:
> > >
> > > -- unknown flag:
> > > -A
> > >
> > >
> > > usage: pmemd [-O] -i mdin -o mdout -p prmtop -c inpcrd -r restrt
> > > [-ref refc -x mdcrd -v mdvel -frc mdfrc -e mden -inf
> mdinfo
> > > -l logfile]
> > > [-ng numgroups -groupfile groupfile -rem remd_method]
> > > [-amd amdlog_name -gamd gamdlog_name -scaledMD
> > > scaledMDlog_name -suffix output_files_suffix]
> > >
> > > ?I want to restart the run from the last .rst file generated?.
> > >
> > > To be more specific, I would like to know how to change my command
> from:
> > >
> > > pmemd.cuda.MPI -O -i run.mdin -p run.parm7 -c run-prev.rst -r run.rst
> -o
> > > run.out -x run.nc
> > >
> > > to a command which restart my simulation? what changes should I do on
> > > run.mdin, run-prev.rst and run.rst so that I can resume run.out and
> > run.nc
> > > ?
> > >
> > > *MIDHUN K MADHU*
> > > Ph.D Student
> > > Dept. of Biological Sciences
> > > IISER Bhopal
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Stephan Schott Verdugo
Biochemist
Heinrich-Heine-Universitaet Duesseldorf
Institut fuer Pharm. und Med. Chemie
Universitaetsstr. 1
40225 Duesseldorf
Germany
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Received on Tue May 22 2018 - 06:00:03 PDT
