分子动力学模拟参考文献
gromacs
HESS B, KUTZNER C, VAN DER SPOEL D, et al. GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation J. Journal of Chemical Theory and Computation, 2008, 4(3): 435-47.
力场
charmm36
amber99SB-ILDN
Lindorff-Larsen K, Piana S, Palmo K, Maragakis P, Klepeis JL, Dror RO, Shaw DE. Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins. 2010 Jun;78(8):1950-8. doi: 10.1002/prot.22711.
amber14SB
J.A. Maier, C. Martinez, K. Kasavajhala, L. Wickstrom, K.E. Hauser and C. Simmerling. (2015) "ff14SB: Improving the accuracy of protein side chain and backbone parameters from ff99SB." J. Chem. Theory Comput. 11, 3696-3713.
amber19SB
TIAN C, KASAVAJHALA K, BELFON K A A, et al. ff19SB: Amino-Acid-Specific Protein Backbone Parameters Trained against Quantum Mechanics Energy Surfaces in Solution J. Journal of Chemical Theory and Computation, 2019, 16(1): 528-52.
GAFF
Wang, J., Wolf, R. M.; Caldwell, J. W.;Kollman, P. A.; Case, D. A. "Development and testing of a general AMBER force field". Journal of Computational Chemistry, 2004 v. 25, 1157-1174.
UFF
Rappe, A. K.; Casewit, C. J.; Colwell, K. S.; Goddard, W. A. III; Skiff, W. M.; "UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations." J Am Chem Soc, 1992 v. 114, 10024-10039.
CGENFF
K Vanommeslaeghe, E Hatcher, C Acharya, S Kundu, S Zhong, J Shim, E Darian, O Guvench, P Lopes, I Vorobyov, and Alexander D MacKerell Jr. CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. J. Comput. Chem., 31(4):671--690, March 2010.
charmm-gui
O S, KIM T, IYER V G, et al. CHARMM-GUI: A web-based graphical user interface for CHARMM J. Journal of Computational Chemistry, 2008, 29(11): 1859-65.