Dear Berk: Thank you so much for the clarification!!! It is so helpful!
Best! Xueming On Fri, Aug 13, 2010 at 4:13 AM, Berk Hess <g...@hotmail.com> wrote: > > > > 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 > > -- > 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 >
-- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
