Cheong Wee Loong, Daniel wrote:
Hi all,
This may be a silly and trivial question, but the energy unit given in
Gromacs is kJ/mol. What I don’t quite understand is, the energy is per
mole of what exactly?
In a very real sense, it doesn't matter. It's just a label for a
convenient bucket of energy for chemistry.
The energy of an isolated water molecule has a certain value, which we
might measure in joules relative to some defined zero. Two such
molecules at infinite separation would have twice that energy, etc. Once
we start approaching Avogadro's number, we would prefer to express that
energy as kJ/mol just for our numerical convenience.
Equally, we could take a water molecule and a methane molecule at
infinite separation, and add their energy... and add lots more... and
get irritated at the size of the number, and just divide by Avogadro for
convenience. The system is no longer homogeneous, but so long as we
compare energies formed in the same way, our conclusions will be valid.
MD force fields are typically parameterized against things like
experimental or computational enthalpies of formation, normally measured
in kJ/mol (unless you're a unlucky enough to be American!). So the
parameters that get derived are conveniently measured in units derived
from kJ/mol. We could convert them to "absolute" joules, but the numbers
would all be stupid. There's a reason quantum chemists work in Hartrees!
Were we to work in absolute joules, the numbers we'd produce then would
still relate to the numbers we actually produce in kJ/mol - by Avogadro.
Mark
The energy is system size dependent, so if I double the number of
molecules, the energy will double accordingly. But then the unit kJ/mol
seems to imply that it is size-independent. So how do I reconcile this?
Also, let’s say I have a protein molecule surrounded by water
molecules. Again in this case, I don’t quite understand what “per mole”
means in this case.
Thanks in advance for any insights you can teach me.
Daniel
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