Re: [AMBER] checkpoint on Amber within batch job

From: Jason Swails <>
Date: Thu, 23 Jan 2014 09:54:55 -0500

On Thu, 2014-01-23 at 13:57 +0000, Zhuang, Yu wrote:
> Hi,
> Thanks for your information. Does this means I just need to re-format the sander command for the next run without modification of .in file? For example,
> Original:
> srun_ps sander.MPI -O -i -o 2q2m_wat_md2.out -c 2q2m_wat_md1.restrt -p 2q2m_wat.prmtop -r 2q2m_wat_md2.restrt -x 2q2m_wat_md2.mdcrd
> step 2 simulation:
> srun_ps sander.MPI -O -i -o 2q2m_wat_md2.out -c 2q2m_wat_md2.restrt -p 2q2m_wat.prmtop -r 2q2m_wat_md3.restrt -x 2q2m_wat_md3.mdcrd

This will work, but remember that the total number of steps will be the
number of steps that finished the first time + the number of steps that
finish the second time. If you want to run for a specific length of
time, you will need to change "nstlim".

Also, you specified the same output file name, so the mdout file from
the second simulation will overwrite the one written in the first. You
can use the -A flag instead of -O to append to existing files, but my
personal preference is to use unique file names for all simulations.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Thu Jan 23 2014 - 07:00:03 PST
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