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Linear Basis Function Approach to Efficient Alchemical Free Energy Calculations. 1. Removal of Uncharged Atomic Sites

''J. Chem. Theory Comput., Vol. 10, No. 3. (31 January 2014), pp. 1128-1149, doi:10.1021/ct4009188''<br /><br />We present a general approach to transform between molecular potential fu...
— Michael Shirts — Date Added: 2015-02-21 21:08:08

On the Efficiency of Exchange in Parallel Tempering Monte Carlo Simulations

''J. Phys. Chem. B, Vol. 109, No. 9. (10 February 2005), pp. 4189-4196, doi:10.1021/jp045073+''<br /><br />We introduce the concept of effective fraction, defined as the expected probab...
— Cristian Ciobanu — Date Added: 2015-02-21 20:45:44

Effects of Temperature Control Algorithms on Transport Properties and Kinetics in Molecular Dynamics Simulations

''J. Chem. Theory Comput., Vol. 9, No. 7. (17 May 2013), pp. 2887-2899, doi:10.1021/ct400109a''<br /><br />Temperature control algorithms in molecular dynamics (MD) simulations are nece...
— Michael Shirts — Date Added: 2015-02-21 20:39:47

Practical Aspects of Free-Energy Calculations: A Review

''J. Chem. Theory Comput., Vol. 10, No. 7. (8 July 2014), pp. 2632-2647, doi:10.1021/ct500161f''<br /><br />Free-energy calculations in the framework of classical molecular dynamics sim...
— Wilfred van Gunsteren — Date Added: 2014-05-25 02:33:50

Accuracy Assessment and Automation of Free Energy Calculations for Drug Design

''J. Chem. Inf. Model., Vol. 54, No. 1. (20 November 2013), pp. 108-120, doi:10.1021/ci4004199''<br /><br />As the free energy of binding of a ligand to its target is one of the crucial...
— Thomas Fox — Date Added: 2013-11-27 21:33:55

Net charge changes in the calculation of relative ligand-binding free energies via classical atomistic molecular dynamics simulation

''J. Comput. Chem. (1 November 2013), pp. n/a-n/a, doi:10.1002/jcc.23490''<br /><br />The calculation of binding free energies of charged species to a target molecule is a frequently en...
— Chris Oostenbrink — Date Added: 2013-11-23 00:50:20

Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: An accurate correction scheme for electrostatic finite-size effects

''Journal of Chemical Physics, Vol. 139, 184103''<br /><br />aip Publishers Publications Topics | Librarians Authors Your access is provided by: Univ of California Irvine Register...
— PH Hünenberger — Date Added: 2013-11-11 22:22:40

Calculation of Free Energy Landscape in Multi-Dimensions with Hamiltonian-Exchange Umbrella Sampling on Petascale Supercomputer

''J. Chem. Theory Comput. In Journal of Chemical Theory and Computation, Vol. 8, No. 11. (20 September 2012), pp. 4672-4680, doi:10.1021/ct300468g''<br /><br />An extremely scalable com...
— Benoît Roux — Date Added: 2013-07-18 23:06:10

Thermodynamic coupling between activation and inactivation gating in potassium channels revealed by free energy molecular dynamics simulations

''The Journal of General Physiology, Vol. 138, No. 6. (01 December 2011), pp. 571-580, doi:10.1085/jgp.201110670''<br /><br />The amount of ionic current flowing through K+ channels is...
— Benoît Roux — Date Added: 2013-07-18 23:03:24

Computations of Standard Binding Free Energies with Molecular Dynamics Simulations

''J. Phys. Chem. B, Vol. 113, No. 8. (15 January 2009), pp. 2234-2246, doi:10.1021/jp807701h''<br /><br />An increasing number of studies have reported computations of the standard (abs...
— Benoît Roux — Date Added: 2013-07-18 23:02:16