[gmx-users] mdrun with append option
Mark Abraham
Mark.Abraham at anu.edu.au
Fri Jan 28 22:20:35 CET 2011
On 29/01/2011 3:56 AM, Sai Pooja wrote:
> Hi,
> I am using tpbconv and mdrun to extend a simulation. I use it with the
> append option but the files still get overwritten or erased. Can
> someone help me in this regard?
> Pooja
> Commands (in python)
> cmd = '(%s/tpbconv -extend %f -s rex_%d.tpr -o rex_%d.tpr)'
> %(GROMPATH,dtstep,i,i)
> os.system(cmd)
> time.sleep(1)
> cmd = 'nbs submit -command "'
> cmd += '(%s/mdrun_mpi -noh -noversion -s rex_%d.tpr -e rex_%d -c
> after_rex_%d -cpi restart%d -cpo restart%d -append -g rexlog%d -x
> rextraj%d >/dev/null); ' %(GROMPATH,i,i,i,i,i,i,i)
> cmd += '" '
> cmd += '-nproc 1 '
> cmd += '-name "GENHAM-DIHEDRAL-%d" '%(i)
> cmd += '-mail start end '
> cmd += '-elapsed_limit 16h >> rexid'
> os.system(cmd)
More useful for diagnostic and record-preservation purposes is to
construct the cmd string and print it to stdout (or something).
At the moment it is far from clear that your -cpi file exists for the
new run.
Mark
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