[gmx-users] mdrun with append option

[Justin A. Lemkul]

Disregard the version question; I see it now in the command string.  You should 
still check for errors, and consider using version 4.5.3 to see if the issue 
persists.

-Justin

Justin A. Lemkul wrote:
> 
> 
> Sai Pooja wrote:
>> 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.
>>
> 
> In theory, there's nothing wrong with what you've done.  What version of 
> Gromacs is this?  Are there any error messages written to the .log file 
> or stdout?  In general, when something goes wrong, Gromacs is fairly 
> vocal about it.
> 
> -Justin
> 
>> On Fri, Jan 28, 2011 at 4:37 PM, Sai Pooja <saipooja at gmail.com 
>> <mailto: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 <mailto: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.
>>
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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