> Date: Thu, 12 Aug 2010 17:33:09 -0400 > From: chris.ne...@utoronto.ca > To: gmx-users@gromacs.org > Subject: [gmx-users] Units of k1 in the pulling code > > Dear Xueming: > > the word "mol" is short form for "mole" > > http://en.wikipedia.org/wiki/Mole_%28unit%29 > > In the pull code context, it refers to moles of the pulled group. > > 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. To clarify this, the force on the COM is not simply applied to each atom, but each atom receives a fraction of the COM force proportional to the mass of the atom divided by the mass of the whole COM group. Berk > > Chris. > > -- original message -- > > Hi there > > The units for pull_k1 = $$ kJ/mol/nm. If this force is applied to a cluster, > the "/mol" in the units of force means per atom in the cluster, or single > molecule composed of several atoms? Sorry, I don't know the default value of > mol in gromacs. Does that mean per molecule? Besides, the force is applied > to the COM of cluster, but in the real pulling process, the force is applied > to each of the molecule in the cluster, or each of the atom in the cluster? > > Thanks in advance! > > Best! > Xueming > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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