Re: Energy values

From: Vermaas, Joshua (
Date: Fri Apr 14 2017 - 17:57:56 CDT

Hi Matt,

The sanest interpretation I think is that if you had a mole number of
systems in this configuration, that is the minimum amount of energy that
needs to be imparted (by lasers? hotplate? wherever really) to break the
two molecules apart and send them to infinity in all systems. There are
627 kcal/mol in 1 hartree, and typical interaction energies between two
small molecules in a quantum system is usually a few thousandth of a
hartree, and these small molecules are what MD force fields are
parameterized against. But you have macromolecules... If the interacting
surface is of any size at all, you have several thousand of these small
interactions adding together (from all the attractive LJ terms that
happen to be within the cutoff), and you have interaction energies that
are legitimately on the scale of hartrees, which appears to us a several
hundred kcal/mol.

So interaction energies are nearly always going to be high for pretty
big molecules that are kinda close together, which is why I always do a
little eye-roll when I see them in MD papers related to binding.
Calculate the interaction energy between one macromolecule and the water
around it. It will also be high. Same for one water and the waters
around it. High and negative interaction energies are pretty standard,
and basically just mean the system won't immediately blow apart. The
interaction energies as calculated in NAMD completely ignore any
screening by intervening water, and is completely oblivious to any sort
of entropy term on its own. If you are aware of those limitations, you
are golden, but I've seen waay too many people get hung up on big
interaction energies as proof of selective binding that I needed to get
on my soapbox. :D


On 04/14/2017 04:02 PM, matthew reeves wrote:
> Hi,
> I've just run a NAMD simulation on two macromolecules and isolated the the interaction energy (VDW + electrostatic). But the interaction energy seems to be ~-800 kcal/mol, which is extremely high considering it is just the interaction energy.
> Would I be correct in assuming that one mole in this case actually represents one mole of the entire system, instead of a mole of atoms? I know this seems like a rather strange question but any assistance would be appreciated.
> Regards
> Matt

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