[gmx-users] Units of k1 in the pulling code

[XUEMING TANG]

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 <gmx3 at hotmail.com> wrote:

>
>
> > Date: Thu, 12 Aug 2010 17:33:09 -0400
> > From: chris.neale at utoronto.ca
> > To: gmx-users at 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
> >
> >
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