Table 3.
Examples of MD software that can be used to perform dynamic docking simulation.
| Software | GPU Support | Biased MD Support | PLUMED 2.3 Patch Available | License |
|---|---|---|---|---|
| MD Engines | ||||
| ACEMD [114] | x | x | x 1 | Free Serial Version (for Academia) |
| AMBER [115] | x | x | x | Paid |
| CHARMM [116] | x | x | Free Serial Version | |
| Desmond [117] | x | x | Free for Academia | |
| DL_POLY [118] | x | x | x 1 | Free for Academia |
| GROMACS [119] | x | x | x | Free |
| LAMMPS [120] | x | x | x | Free |
| NAMD [121] | x | x | x | Free |
| ORAC [122] | x | Free | ||
| Tinker [123] | x | Free | ||
| Software Interfaces | ||||
| BiKi Life Sciences | - | - | - | Paid |
| HTMD | - | - | - | Free Basic Version (for Academia) |
| SEEKR | - | - | - | Free |
1 PLUMED is natively supported by the MD engine.