[gmx-users] mdrun with append option

[Justin A. Lemkul]

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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