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

Bibliography

[1]William L. Jorgensen, Jayaraman Chandrasekhar, Jeffry D. Madura, Roger W. Impey, and Michael L. Klein. Comparison of simple potential functions for simulating liquid water. Journal of Chemical Physics, 79:926–935, 1983.
[2]Hans W. Horn, William C. Swope, Jed W. Pitera, Jeffry D. Madura, Thomas J. Dick, Greg L. Hura, and Teresa Head-Gordon. Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew. Journal of Chemical Physics, 120:9665–9678, 2004.
[3]Gregory D. Hawkins, Christopher J. Cramer, and Donald G. Truhlar. Pairwise solute descreening of solute charges from a dielectric medium. Chemical Physics Letters, 246(1-2):122–129, 1995.
[4]Alexey Onufriev, Donald Bashford, and David A. Case. Exploring protein native states and large-scale conformational changes with a modified generalized Born model. Proteins, 55(22):383–394, 2004.
[5]John Mongan, Carlos Simmerling, J. Andrew McCammon, David A. Case, and Alexey Onufriev. Generalized Born model with a simple, robust molecular volume correction. Journal of Chemical Theory and Computation, 3(1):156–169, 2007.
[6]Hai Nguyen, Daniel R. Roe, and Carlos Simmerling. Improved generalized Born solvent model parameters for protein simulations. Journal of Chemical Theory and Computation, 9(4):2020–2034, 2013.
[7]Michael Schaefer, Christian Bartels, and Martin Karplus. Solution conformations and thermodynamics of structured peptides: molecular dynamics simulation with an implicit solvation model. Journal of Molecular Biology, 284(3):835–848, 1998.
[8]Jay W. Ponder. Personal communication.
[9]Ulrich Essmann, Lalith Perera, Max L. Berkowitz, Tom Darden, Hsing Lee, and Lee G. Pedersen. A smooth particle mesh Ewald method. Journal of Chemical Physics, 103(19):8577–8593, 1995.
[10]Abdulnour Y. Toukmaji and John A. Board Jr. Ewald summation techniques in perspective: a survey. Computer Physics Communications, 95:73–92, 1996.
[11]Ilario G. Tironi, René Sperb, Paul E. Smith, and Wilfred F. van Gunsteren. A generalized reaction field method for molecular dynamics simulations. Journal of Chemical Physics, 102(13):5451–5459, 1995.
[12]Michael R. Shirts, David L. Mobley, John D. Chodera, and Vijay S. Pande. Accurate and efficient corrections for missing dispersion interactions in molecular simulations. Journal of Physical Chemistry B, 111:13052–13063, 2007.
[13]K.K. Wang, J.D. Chodera, Y. Yang, and Michael R. Shirts. Identifying ligand binding sites and poses using gpu-accelerated hamiltonian replica exchange molecular dynamics. Journal of Computed Aided Molecular Design, 27:989, 2013.
[14]S. Boresch, F. Tettinger, M. Leitgeb, and M. Karplus. Absolute binding free energies: a quantitative approach for their calculation. Journal of Physical Chemistry B, 107:9535, 2003.
[15]D.L. Mobley, J.D. Chodera, and K.A. Dill. On the use of orientational restraints and symmetry corrections in alchemical free energy calculations. Journal of Chemical Physics, 125:084902, 2006.
[16]John D. Chodera and Michael R. Shirts. Replica exchange and expanded ensemble simulations as gibbs sampling: simple improvements for enhanced mixing. The Journal of Chemical Physics, 2011. URL: http://scitation.aip.org/content/aip/journal/jcp/135/19/10.1063/1.3660669, doi:http://dx.doi.org/10.1063/1.3660669.