Table 3. Summary of simulation setups used in this study.
Additional simulation details can be found in text section ‘Molecular dynamics simulation details’.
| Studies | Box size (nm3) | Number of Na+ | Number of Mg2+ | Number of Cl− |
|---|---|---|---|---|
| Single nucleosome 100 mM NaCl+0.5 mM MgCl2 | 216,000 | 13,017 | 65 | 13,003 |
| Twelve nucleosomes 5 mM NaCl | 1,331,000 | 6196 | 0 | 4006 |
| Twelve nucleosomes 150 mM NaCl | 216,000 | 21,695 | 0 | 19,505 |
| Twelve nucleosomes 0.6 mM MgCl2 | 3,375,000 | 0 | 2314 | 2438 |
| Twelve nucleosomes 1 mM MgCl2 | 3,375,000 | 0 | 3127 | 4064 |
| Two 147 bp 601-seq nucleosomes 35 mM NaCl+11 mM MgCl2 | 125,000 | 2922 | 828 | 4290 |
| Two 147 bp 601-seq nucleosomes 150 mM NaCl+2 mM MgCl2 | 216,000 | 19,505 | 260 | 19,737 |
| Two 147 bp poly-dA:dT nucleosomes 150 mM NaCl+2 mM MgCl2 | 216,000 | 19,505 | 260 | 19,737 |
| Two 147 bp poly-dG:dC nucleosomes 150 mM NaCl+2 mM MgCl2 | 216,000 | 19,505 | 260 | 19,737 |
| Two 167 bp 601-seq nucleosomes 150 mM NaCl+2 mM MgCl2 | 216,000 | 19,505 | 260 | 19,657 |
| Two 167 bp 601-seq nucleosomes with H1.0 150 mM NaCl+2 mM MgCl2 | 216,000 | 19,505 | 260 | 19,763 |