Table 1.

Approximate relative computational costs of MD calculations using various solvation models in CHARMM (version c34b1) for proteins in the approximate range of 50 to 500 residues in size (750 to 7500 atoms in the all-H representation). The “atomic representation” column indicates whether the solvation model is based on a polar hydrogen (PARAM19) or an all hydrogen (PARAM22) atomic model. (In the TIP3P calculations, this applies only to the protein, since the water model is unchanged). The “outer NB cutoff” column gives the outer cutoff distance for non-bonded interactions recommended for the model. The relative costs, or speeds, of the various solvent models show a much greater variability when they are all compared to a single vacuum calculation on a given system (last column, “actual cost”) than they do when each model is compared to a vacuum calculation that uses the same atomic representation and cutoff distance (fourth column, “intrinsic cost”). See text. The TIP3P results (7,8) are for calculations using 30–60 times as many explicit water molecules as protein residues. The TIP3P calculations have a higher computational cost relative to vacuum when the simpler and faster polar H model is used for the protein. All benchmarking was performed on an Intel Pentium 4 3.20 GHz CPU with an ifort (9.0) CHARMM compilation and repeated on a 1.6 GHz AMD Opteron CPU with a gnu (gcc-4.2) compilation, using a non-bonded list update frequency of 10 steps/update.

	atomic representation	outer NB cutoff (Å)	cost relative to:
			vacuum w/the solvation model- specific cutoff and atomic representation (“intrinsic cost”)	vacuum w/an 8 Å cutoff and a polar H atomic representation (“actual cost”)
1) SASA	polar H	8	1.5–1.9	1.5–1.9
2) EEF1	polar H	10	1.6–1.7	2–3
3) SCPISM	all H	14	1.7	10–16
4) ACE	all H	20	3.5–4.5	60–80
5) GBSW	all H	20	4.5–6	70–100
6) GBMV	all H	20	6–10	100–175
7) TIP3P	all H (solute)	16	20–60	200–500+
8) TIP3P	polar H (solute)	16	50–200	200–500+