**From:** Jeffrey Potoff (*jpotoffx_at_gmail.com*)

**Date:** Wed Dec 12 2012 - 21:46:16 CST

**Next message:**Chris Chipot: "Re: Alchemical transformations and DDG of point mutations"**Previous message:**翁林岽: "understanding the energy term in NAMD log file"**In reply to:**翁林岽: "understanding the energy term in NAMD log file"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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.

Jeff

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 jpotoff_at_wayne.edu 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 http://potoff1.eng.wayne.edu ======================================================================

**Next message:**Chris Chipot: "Re: Alchemical transformations and DDG of point mutations"**Previous message:**翁林岽: "understanding the energy term in NAMD log file"**In reply to:**翁林岽: "understanding the energy term in NAMD log file"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

*
This archive was generated by hypermail 2.1.6
: Tue Dec 31 2013 - 23:22:50 CST
*