. Author manuscript; available in PMC: 2012 Nov 8.

Published in final edited form as: J Chem Theory Comput. 2011 Nov 8;7(11):3635–3642. doi: 10.1021/ct200563j

Table 1.

Total electrostatic energy of benchmark systems. To validate NAMD’s implicit solvent implementation, the total electrostatic energy (in units kcal/mol) of the six benchmark systems was calculated by NAMD and Amber implementations of the GB^OBC implicit solvent;³⁸ error is calculated through eq. 13.

	NAMD	Amber	error
2KKW	−5,271.42	−5,271.23	3.6E-05
2W5U	−6,246.10	−6,245.88	3.5E-05
3EZQ	−94,291.43	−94,288.17	3.4E-05
3AK8	−89,322.23	−89,319.13	3.4E-05
2W49	−396,955.31	−396,941.54	3.4E-05
1IR2	−426,270.23	−426,255.45	3.4E-05