Re: NAMD energy plugin

From: Kenno Vanommeslaeghe (
Date: Wed Jun 04 2014 - 14:10:39 CDT

On 06/04/2014 02:34 PM, Aron Broom wrote:
> 2) Even if you are just comparing to an enthalpy, this is still just a raw
> enthalpy, that is, an H and not a delta-H which is the kind of value you
> would get from an experiment since raw enthalpies are not measurable. So
> you'd need to compare your enthalpy to some reasonable reference, like the
> ligand in water or something.

Exactly, the interaction energy seems to be in the right ballpark for a
vacuum interaction involving charged molecules. Unfortunately, this
quantity is not commonly relevant to actual bio(chem/phys/med)ical
research projects. This is a recurrent question; I really think this list
would benefit from a FAQ (which still wouldn't excuse users from searching
the archives).

Also, does the NAMD/VMD community have a policy regarding posting on
multiple mailinglists at once? Because it is frowned upon in a lot of

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