Re: [AMBER] Restart From Check point File

From: Stephan Schott <>
Date: Sun, 20 May 2018 17:27:10 +0200

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.


2018-05-20 14:47 GMT+02:00 Midhun K Madhu <>:

> 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
> 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
> ?
> Ph.D Student
> Dept. of Biological Sciences
> IISER Bhopal
> _______________________________________________
> AMBER mailing list

Stephan Schott V.
Bioquímico / Licenciado en Bioquímica
AMBER mailing list
Received on Sun May 20 2018 - 08:30:03 PDT
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