MOLECULAR DYNAMICS PERFORMANCE GUIDE - Digital Research Alliance of CANADA

DATASETS

ID Name Files Description Image
1 6n4o

Complex of human Argonaute2 with miR-122.
Number of atoms: 239,131
Number of water molecules: 74595
Number of Na+/Cl- ions: 195/189
Dimensions: 134 x 134 x 134
Force fields: AMBER RNA.OL3 + ff14SB
Water model: TIP3P
Buffer: 0.15 M NaCl solution.

2 4cg1

Complex of cutinase enzyme with p-nitrophenol.
Simulation system for QM/MM benchmarks.
QM site with 27 heavy and 26 hydrogen atoms.
Number of water molecules: 9642
Dimensions: 77 x 79 x 68
Force fields: AMBER ff14SB + gaff
Water model: TIP3P
Data by courtesy of Mohamed Aboelnga

3 9naw

H-1 Parvovirus VLP.
Number of atoms: 3,023,780
Number of water molecules: 836291
Number of Na+/Cl- ions: 2416/1876
Dimensions: 327 x 327 x 327
Force fields: AMBER ff19SB
Water model: OPC
Buffer: 0.15 M NaCl solution