References

Here are a list of references for the various components and algorithms used in YANK.

Todo

Turn this into a hyperlinked bibliography.

YANK

Rizzi A, Grinaway PB, Parton DL, Shirts MR, Wang K, Eastman P, Friedrichs M, Pande VS, Branson K, Mobley DL, Chodera JD. YANK: A GPU-accelerated platform for alchemical free energy calculations. In preparation.

OpenMM GPU-accelerated molecular mechanics library

Friedrichs MS, Eastman P, Vaidyanathan V, Houston M, LeGrand S, Beberg AL, Ensign DL, Bruns CM, and Pande VS. Accelerating molecular dynamic simulations on graphics processing units. J. Comput. Chem. 30:864, 2009. http://dx.doi.org/10.1002/jcc.21209

Eastman P and Pande VS. OpenMM: A hardware-independent framework for molecular simulations. Comput. Sci. Eng. 12:34, 2010. http://dx.doi.org/10.1109/MCSE.2010.27

Eastman P and Pande VS. Efficient nonbonded interactions for molecular dynamics on a graphics processing unit. J. Comput. Chem. 31:1268, 2010. http://dx.doi.org/10.1002/jcc.21413

Eastman P and Pande VS. Constant constraint matrix approximation: A robust, parallelizable constraint method for molecular simulations. J. Chem. Theor. Comput. 6:434, 2010. http://dx.doi.org/10.1021/ct900463w

Eastman P, Friedrichs M, Chodera JD, Radmer RJ, Bruns CM, Ku JP, Beauchamp KA, Lane TJ, Wang LP, Shukla D, Tye T, Houston M, Stich T, Klein C, Shirts M, and Pande VS. OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation. J. Chem. Theor. Comput. 2012. http://dx.doi.org/10.1021/ct300857j

Replica-exchange with Gibbs sampling

Chodera JD and Shirts MR. Replica exchange and expanded ensemble simulations as Gibbs sampling: Simple improvements for enhanced mixing. J. Chem. Phys. 135:19410, 2011. http://dx.doi.org/10.1063/1.3660669

MBAR for estimation of free energies from simulation data

Shirts MR and Chodera JD. Statistically optimal analysis of samples from multiple equilibrium states. J. Chem. Phys. 129:124105, 2008. http://dx.doi.org/10.1063/1.2978177

Long-range dispersion corrections for explicit solvent free energy calculations

Shirts MR, Mobley DL, Chodera JD, and Pande VS. Accurate and efficient corrections or missing dispersion interactions in molecular simulations. J. Phys. Chem. 111:13052, 2007. http://dx.doi.org/10.1021/jp0735987

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