Table 1.2.
The evolution of molecular mechanics and dynamics.
| Trajectory | |||
|---|---|---|---|
| Period | System and Size | [22, 165, 178, 428, 474, 494, 846, 853, 1038, 1067] | |
| 1973 | Dinucleoside (GpC) in vacuum | — | — |
| (8 flexible dihedral angles) | |||
| 1977 | BPTI, vacuum (58 residues, 885 atoms) | 0.01 | |
| 1983 | DNA, vacuum, 12/24 bp (754/1530 atoms) | 0.09 | several weeks each, Vax 780 |
| 1984 | GnRH, vacuum (decapeptide, 161 atoms) | 0.15 | |
| 1985 | Myoglobin, vacuum (1423 atoms) | 0.30 | 50 days, VAX 11/780 |
| 1985 | DNA, 5 bp (2800 atoms) | 0.50 | 20 hrs, Cray X-MP |
| 1989 | Phospholipid Micelle ( ≈ 7,000 atoms) | 0.10 | |
| 1992 | HIV protease (25,000 atoms) | 0.10 | 100 hrs.,Cray Y-MP |
| 1997 | Estrogen/DNA (36,000 atoms, multipoles) | 0.10 | 22 days, HP-735 (8) |
| 1998 | DNA, 24 bp (21,000 atoms, PME) | 0.50 | 1 year, SGI Challenge |
| 1998 | β-heptapeptide in methanol | 200 | 8 months, SGI Challenge (3) |
| ( ≈5000/9000 atoms) | |||
| 1998 | Villin headpiece (36 residues | 1000 | 4 months, 256-proc. Cray T3D/E |
| 12,000 atoms, cutoffs) | |||
| 1999 | bc 1 complex in phospholipid | 1 | 75 days, 64 450-MHz-proc. Cray T3E |
| bilayer (91,061 atoms, cutoffs) | |||
| 2001 | C-terminal β-hairpin of protein- | 38000b | ∼ 8 days, 5000 proc. |
| G (177 atoms, implicit solvent) | Folding@home megacluster | ||
| 2002 | Channel protein in lipid mem- | 5 | 30 hrs, 500 proc. LeMieux terascale |
| brane (106,189 atoms, PME) | system; 50 days, 32 proc. | ||
| Linux (Athlon) | |||
| 2006 | Complete satellite tobacco | 50 | 55 days ( ≈ 1ns/day), 256 Altix nodes |
| mosaic virus (1 million atoms) | NCSA Athlon 2600+ | ||
| NAMD program | |||
| 2007 | B-DNA dodecamer in solvent, PME | 1200 | 130 days, 32 PowerPC BladeCenter |
| AMBER parm98 (15,774 atoms) | proc., MareNostrum Supercomputer | ||
| Barcelona | |||
| 2007 | Villin headpiece (9,684 atoms) | 1000 | 6 months, Folding@home |
| AMBER-2003 | X86 megacluster, GROMACS/MPI | ||
| 2008 | Ubiquitin protein, explicit solvent | 1200 | 14 days (87ns/day), 32 processors |
| OPLS-AA/SPC forcefield, (19,471 atoms) | Operon cluster, Desmond program | ||
| 2008 | Fip35 protein, explicit solvent | 10000 | 14 weeks, NCSA |
| NAMD/CHARMM | Abe cluster, NAMD program | ||
| 2009 | β2AR protein mutants (50,000-99,000 | 2000 | 28 days, 32 (2.66 GHz) E5430 |
| atoms) CHARMM27 forcefield | processors Desmond program |
The examples for each period are representative. The first five systems are modeled in vacuum and the others in solvent. Except for the dinucleoside, simulations refer to molecular dynamics (MD). The two system sizes for the β-heptapeptide [285] reflect two (temperature-dependent) simulations. See text for definitions of abbreviations and further entry information. Length The 38 μs β-hairpin simulation in 2001 represents an ensemble (or aggregate) dynamics simulation, as accumulated over several short runs, rather than one long simulation [1428]. CPU Time/Computer
The computational time is given where possible; estimates for the vacuum DNA, heptapeptide, β-hairpin, and channel protein simulations [285, 746, 1247, 1428] were kindly provided by M. Levitt, W. van Gunsteren, V. Pande, and K. Schulten, respectively.