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On 29/02/2012 9:47 PM, Anna Marabotti wrote:
<blockquote
cite="mid:5E8871D8FECD4DA7A37A908DD2479C80@annabioinforma"
type="cite">
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<div><font face="Arial" size="2"><span class="194583010-29022012">Dear
gmx-users,</span></font></div>
<div><font face="Arial" size="2"><span class="194583010-29022012">I'm
running my simulations on a machine with a queue system that
stops the runs longer than 24 hours. Often, for my
simulations, I need a longer time to complete the runs. </span></font><font
face="Arial" size="2"><span class="194583010-29022012">Let's
have an example. I have to run a 100ns-long simulation on a
machine that produces 10ns/days simulation. I have two
possibilities:</span></font></div>
<div><span class="194583010-29022012"></span> </div>
<div><span class="194583010-29022012"><font face="Arial" size="2">First
approach:</font></span></div>
<div><span class="194583010-29022012"><font face="Arial" size="2">I'm
setting within the .mdp file a global duration of 100 ns.
Then:</font></span></div>
<div><span class="194583010-29022012"><font face="Arial" size="2">grompp
-f param.mdp -c prot.gro -p topol.top -o input_fullMD.tpr</font></span></div>
<div><span class="194583010-29022012"><font face="Arial" size="2">mdrun
-s input_fullMD.tpr -deffnm output_fullMD</font></span></div>
<div><span class="194583010-29022012"><font face="Arial" size="2">After
24 h, I see that the run has been stopped after 10 ns. I
have the output_fullMD.cpt file. Then, I do:</font></span></div>
<div><span class="194583010-29022012"><font face="Arial" size="2">mdrun
-s input_fullMD.tpr -cpi output_fullMD.cpt -deffnm
output_fullMD_2</font></span></div>
<div><span class="194583010-29022012"><font face="Arial" size="2">and
so on for 10 days, until the run has been completed (then I
will concatenate the .xtc, .edr, .trr files)</font></span></div>
</blockquote>
<br>
Yep, or use the same -deffnm filename and -append for more
simplicity. See <a
href="http://www.gromacs.org/Documentation/How-tos/Doing_Restarts#section_2">http://www.gromacs.org/Documentation/How-tos/Doing_Restarts#section_2</a><br>
<br>
<blockquote
cite="mid:5E8871D8FECD4DA7A37A908DD2479C80@annabioinforma"
type="cite">
<div><span class="194583010-29022012"></span> </div>
<div><span class="194583010-29022012"><font face="Arial" size="2">Second
approach:</font></span></div>
<div><span class="194583010-29022012"><font face="Arial" size="2">I'm
setting within the .mdp file a global duration of 10 ns.
Then (as above):</font></span></div>
<div><span class="194583010-29022012"><font face="Arial" size="2">
<div><span class="194583010-29022012"><font face="Arial"
size="2">grompp -f param.mdp -c prot.gro -p topol.top
-o input_fullMD.tpr</font></span></div>
<div><span class="194583010-29022012"><font face="Arial"
size="2">mdrun -s input_fullMD.tpr -deffnm
output_fullMD</font></span></div>
<div><span class="194583010-29022012">After 24 h, the run
has been finished. Then, I continue the run for other 10
ns with:</span></div>
<div><span class="194583010-29022012">tpbconv -s
input_fullMD.tpr -extend 10000 -o input_fullMD_2.tpr </span></div>
<div><span class="194583010-29022012">mdrun -s
input_fullMD_2.tpr -cpi output_fullMD.cpt -deffnm
output_fullMD_2</span></div>
<div><span class="194583010-29022012">and so on for 10 days,
until the 100-ns run has been completed.</span></div>
<div><span class="194583010-29022012"></span> </div>
<div><span class="194583010-29022012">Are the two procedure
producing EXACTLY the same results, or not?</span></div>
</font></span></div>
</blockquote>
<br>
In principle, they are implementing the same algorithm over the 10
runs. In practice, the discussion at <a
href="http://www.gromacs.org/Documentation/Terminology/Reproducibility">http://www.gromacs.org/Documentation/Terminology/Reproducibility</a>
applies and you will likely not observe an identical trajectory from
each case. In theory, mdrun -reprod does a better job in many cases
for often losing performance, but random number states are not
preserved, so various algorithms cannot be reproducible across
restarts.<br>
<br>
<blockquote
cite="mid:5E8871D8FECD4DA7A37A908DD2479C80@annabioinforma"
type="cite">
<div><span class="194583010-29022012"><font face="Arial" size="2">
<div><span class="194583010-29022012"> Which is the best
preferred procedure?</span></div>
</font></span></div>
</blockquote>
<br>
The first, with appending, is simple and requires no concatenation
post-processing. Feel free to back up your files between runs if you
want insurance against loss - but you should do that anyway.<br>
<br>
Anything else requires you to do more work later on for no gain.<br>
<br>
Mark<br>
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