<div>This is the command:</div>
<div> </div>
<div>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<br>pend -g rexlog3 -x rextraj3);" -nproc 1 -name "GENHAM-DIHEDRAL-3" -mail start end</div>
<div> </div>
<div>Pooja<br><br></div>
<div class="gmail_quote">On Fri, Jan 28, 2011 at 4:20 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div>
<div></div>
<div class="h5">On 29/01/2011 3:56 AM, Sai Pooja wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Hi,<br>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?<br>
Pooja<br>Commands (in python)<br>cmd = '(%s/tpbconv -extend %f -s rex_%d.tpr -o rex_%d.tpr)' %(GROMPATH,dtstep,i,i)<br> os.system(cmd)<br> time.sleep(1)<br> cmd = 'nbs submit -command "'<br>
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)<br> cmd += '" '<br>
cmd += '-nproc 1 '<br> cmd += '-name "GENHAM-DIHEDRAL-%d" '%(i)<br> cmd += '-mail start end '<br> cmd += '-elapsed_limit 16h >> rexid'<br> os.system(cmd)<br>
</blockquote><br></div></div>More useful for diagnostic and record-preservation purposes is to construct the cmd string and print it to stdout (or something).<br><br>At the moment it is far from clear that your -cpi file exists for the new run.<br>
<br>Mark<br><font color="#888888">-- <br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
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