Libra: An open-source "Methodology Discovery" Library

Fewest Switches Surface Hopping (FSSH)

Tully, J. C. Molecular Dynamics with Electronic Transitions. J. Chem. Phys. 1990, 93, 1061–1071.

Src: dyn/tsh_prob_fssh.cpp dyn/methods_tsh.cpp

Global Flux Surface Hopping (GFSH)

Wang, L.; Trivedi, D.; Prezhdo, O. V. Global Flux Surface Hopping Approach for Mixed Quantum-Classical Dynamics. J. Chem. Theory Comput. 2014, 10, 3598–3605.

Src: dyn/tsh_prob_gfsh.cpp dyn/methods_tsh.cpp

Markov State Surface Hopping (MSSH)

Tully, J. C.; Preston, R. K. Trajectory Surface Hopping Approach to Nonadiabatic Molecular Collisions: The Reaction of H+ with D2. J. Chem. Phys. 1971, 55, 562–572.

Akimov, A. V.; Trivedi, D.; Wang, L.; Prezhdo, O. V. Analysis of the Trajectory Surface Hopping Method from the Markov State Model Perspective. J. Phys. Soc. Jpn. 2015, 84, 094002.

Src: dyn/tsh_prob_mssh.cpp dyn/methods_tsh.cpp

Nuclear dynamics: Verlet (velocity form) algorithm

Verlet, L. Computer “Experiments” on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules. Phys. Rev. 1967, 159, 98–103.

Src: dyn/Verlet.cpp dyn/Verlet_nvt.cpp dyn/Dynamics_Nuclear.cpp dyn/nuclear/Nuclear.cpp scripts/state/State_methods1.cpp scripts/state/State_methods2.cpp

Nuclear dynamics: Entangled Trajectories Hamiltonian Dynamics (ETHD)

Smith, B.; Akimov, A. V. Entangled Trajectories Hamiltonian Dynamics for Treating Quantum Nuclear Effects. The Journal of Chemical Physics 2018, 148 (14), 144106.

Src: dyn/Verlet.cpp dyn/Verlet_nvt.cpp hamiltonian/nHamiltonian_Generic/nHamiltonian_compute_ETHD.cpp

Electron-Nuclear dynamics: Ehrenfest Dynamics

Akimov, A. V. Libra: An Open-Source “Methodology Discovery” Library for Quantum and Classical Dynamics Simulations. J. Comput. Chem. 2016, 37, 1626–1649.

Theory and derivations: Ehrenfest.pdf

Src: dyn/Ehrenfest.cpp

Rigid body dynamics: Numerically exact integration algorithm

Hernandez de la Pena, L.; van Zon, R.; Schofield, J.; Opps, S. B. "Discontinuous molecular dynamics for semiflexible and rigid bodies" J. Chem. Phys. 2007, 126, 074105

van Zon, R.; Schofield, J. "Numerical implementation of the exact dynamics of free rigid bodies" J. Comp. Phys. 2007, 225, 145-164

Src: dyn_rigidbody/RigidBody_methods5_1.cpp

Rigid body dynamics: DLML (Dullweber-Leimkuhler-McLahlan) algorithm

Dullweber, A.; Leimkuhler, B.; McLachlan, R."Symplectic splitting methods for rigid body molecular dynamics" J. Chem. Phys. 1997, 107, 5840-5851

Src: dyn_rigidbody/RigidBody_methods5_2.cpp

Rigid body dynamics: NO_SQUISH algorithm

Miller, T. F.; Eleftheriou, M.; Pattnaik, P.; Ndirango, A.; Newns, D.; Martyna, G. J. Symplectic Quaternion Scheme for Biophysical Molecular Dynamics. J. Chem. Phys. 2002, 116, 8649–8659.

Src: dyn_rigidbody/RigidBody_methods5_3.cpp

Rigid body dynamics: KLN algorithm

Kamberaj, H.; Low, R. J; Neal, M. P. "Time reversible and symplectic integrators for molecular dynamics simulations of rigid molecules" J. Chem. Phys. 2005, 122, 224114-1 - 224114-30

Src: dyn_rigidbody/RigidBody_methods5_4.cpp

Rigid body dynamics: Terec and qTerec algorithm

Akimov, A. V.; Kolomeisky, A. B. Recursive Taylor Series Expansion Method for Rigid-Body Molecular Dynamics. J. Chem. Theory Comput. 2011, 7, 3062–3071.

Src: dyn_rigidbody/RigidBody_methods5_5.cpp

Rigid body dynamics: Algorithm of Omelyan

Omelyan I. P. "Algorithm for numerical integration of the rigid-body equations of motion" Phys. Rev. E. 1998, 58, 1169-1172

Src: dyn_rigidbody/RigidBody_methods5_6.cpp

Barostat: KLN algorithm (for rigid bodies or all-atomic dynamics)

Both isotropic dilation/contraction and anisotropic (flexible cell) modes are possible

Kamberaj, H.; Low, R. J; Neal, M. P. "Time reversible and symplectic integrators for molecular dynamics simulations of rigid molecules" J. Chem. Phys. 2005, 122, 224114-1 - 224114-30

Src: dyn/barostat/Barostat_methods.cpp

Thermostat: Nose-Hoover thermostat according to the KLN algorithm (for rigid bodies or all-atomic dynamics)

Hoover, W. G. Nose-Hoover Nonequilibrium Dynamics and Statistical Mechanics. Mol. Simul. 2007, 33, 13–19.

Kamberaj, H.; Low, R. J; Neal, M. P. "Time reversible and symplectic integrators for molecular dynamics simulations of rigid molecules" J. Chem. Phys. 2005, 122, 224114-1 - 224114-30

Src: dyn/thermostat/Thermostat_methods.cpp scripts/state/State_methods1.cpp scripts/state/State_methods2.cpp

Thermostat: Nose-Poincare thermostat

Nose, S. An Improved Symplectic Integrator for Nose-Poincare Thermostat. J. Phys. Soc. Jpn. 2001, 70, 75–77.

Bond, S. D.; Leimkuhler, B. J.; Laird, B. B. The Nosé-Poincaré Method for Constant Temperature Molecular Dynamics. J. Comput. Phys. 1999, 151, 114–134.

Kleinerman, D. S.; Czaplewski, C.; Liwo, A.; Scheraga, H. A. Implementations of Nosé–Hoover and Nosé–Poincaré Thermostats in Mesoscopic Dynamic Simulations with the United-Residue Model of a Polypeptide Chain. J. Chem. Phys. 2008, 128, 245103.

Src: dyn/thermostat/Thermostat_methods.cpp scripts/state/State_methods1.cpp scripts/state/State_methods2.cpp

Basic Molecular Mechanics Potentials

Re-usable functions that can be utilized on their own or within a given force field

Src: hamiltonian/Hamiltonian_Atomistic/Hamiltonian_MM pot

Ewald-type lattice sums for electrostatic (1/R) and dispersion (1/R^6) interactions

Karasawa, N.; Goddard III, W. A. Acceleration of Convergence for Lattice Sums. J. Phys. Chem. 1989, 93, 7320–7327.

Procacci, P.; Marchi, M. "Taming the Ewald sum in molecular dynamics simulations of solvated proteins via a multiple time step algorithm" J.Chem.Phys. 1996, 104, 3003-3012

Komeiji, Y. "Ewald summation and multiple time step methods for molecular dynamics simulation of biological molecules" J. Mol. Struct. (Theochem) 2000, 530, 237-243

Src: pot/Potentials_mb_elec.cpp pot/Potentials_mb_vdw.cpp

Charge Equilibration approach (qEQ)

Rappe, A. K.; Goddard, W. A. Charge Equilibration for Molecular Dynamics Simulations. J. Phys. Chem. 1991, 95, 3358–3363.

Src: solvers/qeq

Verlet and Neighbor Cell Lists. Simulation cell variables

Needed to execute efficient MM calculations in periodic systems.

Src: cell

Force Field: DREIDING force field

Mayo, S. L.; Olafson, B. D.; Goddard, W. A. DREIDING: A Generic Force Field for Molecular Simulations. Journal of Physical Chemistry 1990, 94, 8897–8909.

Src: forcefield hamiltonian/Hamiltonian_Atomistic/Hamiltonian_MM

Force Field: Tripos 5.2 force field

Clark, M.; Cramer III, R. D.; Van Opdenbosch, N. Validation of the General Purpose Tripos 5.2 Force Field. J. Comput. Chem. 1989, 10, 982–1012.

Src: forcefield hamiltonian/Hamiltonian_Atomistic/Hamiltonian_MM

Force Field: UFF (Universal Force Field)

Rappe, A. K.; Casewit, C. J.; Colwell, K. S.; Goddard III, W. A.; Skiff, W. M. UFF, a Full Periodic Table Force Field for Molecular Mechanics and Molecular Dynamics Simulations. J. Am. Chem. Soc. 1992, 114, 10024–10035.

Src: forcefield hamiltonian/Hamiltonian_Atomistic/Hamiltonian_MM

Force Field: GAFF (General Amber Force Field)

Wang, J.; Wolf, R. M.; Caldwell, J. W.; Kollman, P. A.; Case, D. A. Development and Testing of a General Amber Force Field. J. Comput. Chem. 2004, 25, 1157–1174.

Src: forcefield hamiltonian/Hamiltonian_Atomistic/Hamiltonian_MM

Force Field: MMFF94 (Merck Force Field)

Halgren, T. A. Merck Molecular Force Field. I. Basis, Form, Scope, Parameterization, and Performance of MMFF94. J. Comput. Chem. 1996, 17, 490–519.

Halgren, T. A. Merck Molecular Force Field. II. MMFF94 van Der Waals and Electrostatic Parameters for Intermolecular Interactions. J. Comput. Chem. 1996, 17, 520–552.

Src: forcefield hamiltonian/Hamiltonian_Atomistic/Hamiltonian_MM