[gmx-users] mdrun with append option

[Sai Pooja]

This is the command:

nbs submit -command "(/usr/local/gromacs/4.5.1/bin/mdrun_mpi -s rex_3.tpr -e
rex_3 -c after_rex_3 -cpi restart3 -cpo restart3 -ap
pend -g rexlog3 -x rextraj3);" -nproc 1 -name "GENHAM-DIHEDRAL-3" -mail
start end

Pooja

On Fri, Jan 28, 2011 at 4:20 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

>  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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