**From:** 翁林岽 (*wenglindong_at_yahoo.com.cn*)

**Date:** Wed Dec 12 2012 - 20:46:31 CST

**Next message:**Jeffrey Potoff: "Re: understanding the energy term in NAMD log file"**Previous message:**Gianluca Interlandi: "Re: Alchemical transformations and DDG of point mutations"**Next in thread:**Jeffrey Potoff: "Re: understanding the energy term in NAMD log file"**Reply:**Jeffrey Potoff: "Re: understanding the energy term in NAMD log file"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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

**Next message:**Jeffrey Potoff: "Re: understanding the energy term in NAMD log file"**Previous message:**Gianluca Interlandi: "Re: Alchemical transformations and DDG of point mutations"**Next in thread:**Jeffrey Potoff: "Re: understanding the energy term in NAMD log file"**Reply:**Jeffrey Potoff: "Re: 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
*