[gmx-users] Units of k1 in the pulling code
chris.neale at utoronto.ca
chris.neale at utoronto.ca
Thu Aug 12 23:33:09 CEST 2010
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
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