[AMBER] Restart From Check point File

From: Midhun K Madhu <midhunk16.iiserb.ac.in>
Date: Sun, 20 May 2018 18:17:24 +0530

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:

  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]

‚ÄčI want to restart the run from the last .rst file generated‚Äč.

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 ?

Ph.D Student
Dept. of Biological Sciences
IISER Bhopal
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Received on Sun May 20 2018 - 06:00:12 PDT
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