[gmx-users] mdrun with append option

[Sai Pooja]

I would be happy to supply more information.. if someone could please look
into this.. otherwise I will have to switch to storing every file and then
just concatenating them which seems like a rather roundabout way of doing
it.

On Fri, Jan 28, 2011 at 4:37 PM, Sai Pooja <saipooja at gmail.com> wrote:

> 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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>
>
>
>  --
> Quaerendo Invenietis-Seek and you shall discover.
>



-- 
Quaerendo Invenietis-Seek and you shall discover.
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