Re: understanding the energy term in NAMD log file

From: Jeffrey Potoff (
Date: Wed Dec 12 2012 - 21:46:16 CST

The energy you get out of NAMD is extensive, that is, it depends on the
size of the system. For a given density, e.g. if you run 2x as many
particles, you are going to get 2x the energy. The only way to get a
number that is intensive (invariant with system size) is to normalize
with the number of particles in the system, as it looks like you have
figured out.


On 12/12/2012 9:46 PM, 翁林岽 wrote:
> Hi, all,
> I got confused about the energy value of the NAMD log file and the
> value given by the literature. For example, for the pure Argon fluids,
> the literature gives the potential energy of ~5.4 kJ/mol, while under
> the same simulation conditions, the potential energy given by my
> simulation is ~844.8 kcal/mol. There is a huge difference there. But
> when I divided 844.8 by the total number of Ar atoms (729) in my
> simulation system, the calculated potential energy becomes 1.16
> kcal/mol (i.e., ~4.8 kJ/mol) which is quite near the literature value.
> I don't know whether such a calculation is reasonable.
> As I found in the NAMD mail list, it was said that the unit of energy
> term in the log file was kcal/(mol of systems), so, probably, when we
> divide the value directly given by the log file by the total number of
> molecules in the system, we can get the value in the unit of kcal/(mol
> of solutions or sth.).
> Any suggestions about the thought? Thanks.
> Lindong

Jeffrey J. Potoff
Associate Professor			  Wayne State University		
Department of Chemical Engineering and Materials Science
5050 Anthony Wayne Dr			  Phone:(313)577-9357		
Detroit, MI 48202  	                  Fax:  (313)578-5815

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