. Author manuscript; available in PMC: 2011 Jun 17.

Published in final edited form as: J Chem Theory Comput. 2010 Jun 17;6(7):2214–2224. doi: 10.1021/ct100145f

Table 5. Computational timing and memory resources using PB-SAM for capsid assembly.

Self-polarization of 1YC6 monomer and mutual polarization of 60 monomers of BMV capsid for various dielectric representations (Figure 3)

Number and median sphere radius	Poles	Time to calculate surface integrals [s]	Self-polarization		Mutual-polarization
Number and median sphere radius	Poles	Time to calculate surface integrals [s]	Time [s]	Memory [GB]	Time [s]	Memory [GB]
107 spheres	40	1,083	280	3.6	2,589	4.4^**
4.40 Å	50	4,131	552	7.2
	60	12,336	1,180	13.3
354 spheres	30	423	603	7.8
3.06 Å	40	2,380	2,091	7.1^**	9,365	13.5^**
	50	9,079	4,934	17.1^**
712 spheres	20	70	271	8.6
1.91 Å	30	802	1,177	17.5	16,046	33.8^**
	40	4,508	3,707	14.2^**

^**

memory-saving mode