[gmx-users] mdrun with append option

[Mark Abraham]

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