Re: total mol calculation

From: Peter Freddolino (
Date: Thu Jul 20 2006 - 08:18:00 CDT

Hi Jackie,
two notes. First of all, if you *really* want the total energy present
in your system, you'll have to note that the energies being reported are
in kcal/mol of your system. NAMD doesn't really know what a mol of a
compound is, so if you take a box of water, and compare its energy to
that of another box of water twice the size, you'll get twice the
energy. The "per mol" is just being used as a scaling factor for the
energy. Thus, if you just want the energy of the present system in kcal,
just divide your number of kcal/mol by Avagadro's number (I don't really
understand why you'd need to do this though, since the per mol just
serves as a scaling factor anyway).

Second, please remember that MD energies don't include entropy unless
you do umbrella sampling or something along those lines; I don't know if
that's important for your application or not.


Jackie wrote:
> Hi all,
> Sorry about this, I imagine this answer is pretty straightforward,
> however, I just want to make sure I'm doing this right. I would like
> to calculate adsorption energy for a system and a part of that
> equation requires that I use total energy. If namd gives the values
> of Total energy in kcal/mol, how do I calculate the total number of
> mols to multiply the toal energy by to end up with kcal? For example,
> if there is water and gold. Do I just add up the number of mols of
> water to the number of mols of gold together and then multiply? How do
> I find this?
> Thanks!
> Jackie
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