Table 6.
Comparison of Lennard-Jones parameters for key atom types in the commercial CHARMm and academic CHARMM force field. (See caption of Table 1 for details.) Note that the academic parameters are the same for the NH1, NH2 and NH3 atom types, as indicated in the table, and that the commercial CT atom type maps to academic CT1 if the carbon has one hydrogen and to CT2 if it has two hydrogens. We also used CT1 parameters for an aliphatic carbon with no hydrogens.
| Commercial |
Academic |
|||||
|---|---|---|---|---|---|---|
| Name | ε | σ | Name | ε | σ | |
| Ferrocenes | ||||||
| Cyclopentadiene C | C5R | 0.0500 | 2.040 | CA | 0.0700 | 1.9924 |
| Cyclopentadiene H | HA | 0.0420 | 1.330 | HP | 0.0300 | 1.3582 |
| Ammonium N | NT | 0.1500 | 1.650 | NH1/NH2/NH3 | 0.2000 | 1.850 |
| Ammonium C | CT | 0.0903 | 1.800 | CT3 | 0.0800 | 2.060 |
| Ammonium H | HA | 0.0420 | 1.330 | HA | 0.0220 | 1.320 |
| Bicyclooctanes and Adamantanes | ||||||
| C | CT | 0.0903 | 1.800 | CT1 CT2 |
0.0200, 0.0550 |
2.275, 2.175 |
| Aliphatic H | HA | 0.0420 | 1.330 | HA | 0.0220 | 1.320 |
| N | NT | 0.1500 | 1.650 | NH3 | 0.2000 | 1.850 |
| Ammonium H | HC | 0.0498 | 0.600 | HC | 0.0460 | 0.2245 |
| CB[7] | ||||||
| Carbonyl O | O | 0.1591 | 1.550 | O | 0.1200 | 1.700 |
| Carbonyl C | C | 0.1410 | 1.870 | CC | 0.0700 | 2.000 |
| N | NX | 0.0999 | 1.830 | NH1/NH2/NH3 | 0.2000 | 1.850 |
| Other Cs | CT | 0.0903 | 1.800 | CT1 CT2 |
0.0200 0.0550 |
2.275 2.175 |
| H | HA | 0.042 | 1.330 | HA | 0.0220 | 1.320 |