Desmond
Desmond [1] [2] [3] High-performance molecular dynamics simulations for biomolecular systems. Has CHARMM, AMBER, and OPLS force fields.
References
- ↑ Devleena Shivakumar, Joshua Williams, Yujie Wu, Wolfgang Damm, John Shelley and Woody Sherman "Prediction of Absolute Solvation Free Energies using Molecular Dynamics Free Energy Perturbation and the OPLS Force Field", Journal of Chemical Theory and Computation 6 pp. 1509-1519 (2010)
- ↑ Zuojun Guo, Udayan Mohanty, Justin Noehre, Tomi K. Sawyer, Woody Sherman and Goran Krilov "Probing the α-Helical Structural Stability of Stapled p53 Peptides: Molecular Dynamics Simulations and Analysis", Chemical Biology & Drug Design 75 pp. 348-359 (2010)
- ↑ Kevin J. Bowers, Edmond Chow, Huafeng Xu, Ron O. Dror, Michael P. Eastwood, Brent A. Gregersen, John L. Klepeis, Istvan Kolossvary, Mark A. Moraes, Federico D. Sacerdoti, John K. Salmon, Yibing Shan, David E. Shaw "Scalable algorithms for molecular dynamics simulations on commodity clusters", Proceedings of the 2006 ACM/IEEE conference on Supercomputing Article No.: 84 November 11-17 (2006)