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

Berk Hess gmx3 at hotmail.com
Fri Aug 13 10:13:31 CEST 2010

> 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.


> 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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