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

[chris.neale at utoronto.ca]

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.

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