Dear Berk:<div><br></div><div>Thank you so much for the clarification!!! It is so helpful!</div><div><br></div><div>Best!</div><div>Xueming </div><div><br><div class="gmail_quote">On Fri, Aug 13, 2010 at 4:13 AM, Berk Hess <span dir="ltr"><<a href="mailto:gmx3@hotmail.com">gmx3@hotmail.com</a>></span> wrote:<br>
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<br><br>> Date: Thu, 12 Aug 2010 17:33:09 -0400<br>> From: <a href="mailto:chris.neale@utoronto.ca" target="_blank">chris.neale@utoronto.ca</a><br>> To: <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
> Subject: [gmx-users] Units of k1 in the pulling code<div class="im"><br>> <br>> 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 <br>> the force is determined based on the COM distance, and then the force <br>
> is applied to each atom in the pull groups.<br><br></div>To clarify this, the force on the COM is not simply applied to each atom,<br>but each atom receives a fraction of the COM force proportional to the mass<br>of the atom divided by the mass of the whole COM group.<br>
<font color="#888888"><br>Berk</font><div class="im"><br><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>> <br>> <br>> -- <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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