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