[gmx-users] mdrun with append option

Mark Abraham Mark.Abraham at anu.edu.au
Sun Jan 30 00:52:09 CET 2011

On 30/01/2011 10:39 AM, 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.

As I suggested a few emails ago, are you sure that -cpi file exists? If 
your numerical suffixes are indexing restarts, then unless you've done 
some manual copying that you haven't told us about, it won't. Your 
filename scheme seems a bit contorted - like you're trying to do the 
work that GROMACS 4.5.x will just do for you if you let it.

Otherwise, you'll have to do some detective work with gmxcheck on the 
-cpi to see what might be the issue.

In your case, an initial

mdrun -deffnm rex_3

(perhaps save some copies while you're experimenting) and subsequently

tpbconv -extend <blah> -f rex_3 -o rex_3
mdrun -deffnm rex_3 -append

will work and be much simpler than whatever you're trying to do with 
filenames :-)


> 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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