Dear Chris:<div><br></div><div>Thank you very much for it! </div><div><br></div><div>Best!</div><div>Xueming<br><br><div class="gmail_quote">On Thu, Aug 12, 2010 at 5:33 PM, <span dir="ltr"><<a href="mailto:chris.neale@utoronto.ca">chris.neale@utoronto.ca</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Dear Xueming:<br>
<br>
the word "mol" is short form for "mole"<br>
<br>
<a href="http://en.wikipedia.org/wiki/Mole_%28unit%29" target="_blank">http://en.wikipedia.org/wiki/Mole_%28unit%29</a><br>
<br>
In the pull code context, it refers to moles of the pulled group.<br>
<br>
The force is not "applied" to the COM of a cluster. The magnitude of the force is determined based on the COM distance, and then the force is applied to each atom in the pull groups.<br>
<br>
Chris.<br>
<br>
-- original message --<br>
<br>
Hi there<br>
<br>
The units for pull_k1 = $$ kJ/mol/nm. If this force is applied to a cluster,<br>
the "/mol" in the units of force means per atom in the cluster, or single<br>
molecule composed of several atoms? Sorry, I don't know the default value of<br>
mol in gromacs. Does that mean per molecule? Besides, the force is applied<br>
to the COM of cluster, but in the real pulling process, the force is applied<br>
to each of the molecule in the cluster, or each of the atom in the cluster?<br>
<br>
Thanks in advance!<br>
<br>
Best!<br>
Xueming<br><font color="#888888">
<br>
<br>
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