Table 1.
The most used software and force fields for MD simulation of CD complexes.
| N° | Software/Code | Force Field | License | Ref. |
|---|---|---|---|---|
| 1 | GROMACS | GROMOS CHARMM Carbohydrate Solution force field, CSFF (for CD) |
General Public License (GPL) | [32] |
| 2 | AMBER | GAFF, Glycam06 (for CD), q4md-CD (for CD) |
Commercial | [33] |
| 3 | CHARMM | CHARMM FF | Commercial | [34] |
| 4 | Desmond (Schrödinger, Inc.) | OPLS | Commercial | [35] |
| 5 | NAMD | CHARMM | Commercial, academic | [36] |
| 6 | Forcite (BIOVIA Materials Studio, Accelrys) |
COMPASS | Commercial | [37] |