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On 30/01/2011 10:39 AM, Sai Pooja wrote:
<blockquote
cite="mid:AANLkTi=q3Nru+Nq0dt193MNvWtqjqcUtCGj3ep2aGU55@mail.gmail.com"
type="cite">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.<br>
</blockquote>
<br>
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.<br>
<br>
Otherwise, you'll have to do some detective work with gmxcheck on
the -cpi to see what might be the issue.<br>
<br>
In your case, an initial<br>
<br>
mdrun -deffnm rex_3<br>
<br>
(perhaps save some copies while you're experimenting) and
subsequently<br>
<br>
tpbconv -extend <blah> -f rex_3 -o rex_3<br>
mdrun -deffnm rex_3 -append<br>
<br>
will work and be much simpler than whatever you're trying to do with
filenames :-)<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:AANLkTi=q3Nru+Nq0dt193MNvWtqjqcUtCGj3ep2aGU55@mail.gmail.com"
type="cite">
<br>
<div class="gmail_quote">On Fri, Jan 28, 2011 at 4:37 PM, Sai
Pooja <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:saipooja@gmail.com">saipooja@gmail.com</a>></span>
wrote:<br>
<blockquote style="border-left: 1px solid rgb(204, 204, 204);
margin: 0px 0px 0px 0.8ex; padding-left: 1ex;"
class="gmail_quote">
<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>
<font color="#888888">
<div>Pooja<br>
<br>
</div>
</font>
<div>
<div class="h5">
<div class="gmail_quote">On Fri, Jan 28, 2011 at 4:20 PM,
Mark Abraham <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au"
target="_blank">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
<blockquote style="border-left: 1px solid rgb(204, 204,
204); margin: 0px 0px 0px 0.8ex; padding-left: 1ex;"
class="gmail_quote">
<div>
<div>On 29/01/2011 3:56 AM, Sai Pooja wrote:<br>
<blockquote style="border-left: 1px solid rgb(204,
204, 204); margin: 0px 0px 0px 0.8ex;
padding-left: 1ex;" class="gmail_quote">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>
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</font></blockquote>
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<br>
<br clear="all">
<br>
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</div>
<div>
<div class="h5">-- <br>
Quaerendo Invenietis-Seek and you shall discover.<br>
</div>
</div>
</blockquote>
</div>
<br>
<br clear="all">
<br>
-- <br>
Quaerendo Invenietis-Seek and you shall discover.<br>
</blockquote>
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