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<br><br>> Date: Thu, 12 Aug 2010 17:33:09 -0400<br>> From: chris.neale@utoronto.ca<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] Units of k1 in the pulling code<br>> <br>> Dear Xueming:<br>> <br>> the word "mol" is short form for "mole"<br>> <br>> http://en.wikipedia.org/wiki/Mole_%28unit%29<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>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><br>Berk<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 gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br> </body>
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