Molecular dynamics , potential energy

Bash, P.A., Field, M.J.,Karplus, M. Free energy perturbation method for chemical reactions in the condensed phase A dynamical approach baaed on a combined quantum and molecular dynamics potential. J. Am. Chem. Soc. 109 (1987) 8092-8094. 

Ding YB, Bernardo DN, Kroghjespersen K, Levy RM (1995) Solvation free-energies of small amides and amines from molecular-dynamics free-energy perturbation simulations using pairwise additive and many-body polarizable potentials. J Phys Chem 99(29) 11575—11583... 

Solvation Free Energies of Small Amides and Amines from Molecular Dynamics/Free Energy Perturbation Simulations Using Pairwise Additive and Many-Body Polarizable Potentials. 

H. Liu, F. Mulle Plathe, and W. F. van Gunsteren, /. Chem. Phys., 102, 1702 (1995). A Molecular Dynamics Simulation Study with a Combined Quantum Medianical and Molecular Mechanical Potential Energy Function Solvation Effects of the Conformational Equilibrium of Dimethoxyethane. 

Chakraborty A, Zhao Y, Lin H, Tiuhlm DG (2006) Combined valence bond-molecular mechanics potential-energy surface tmd direct dynamics study of rate constants and kinetic isotope effects for the H + C2H6 reaction. J Chem Phys 124 044315... 

One obvious remedy for this problem is to choose time-step lengths so as to avoid small integer multiples of half-periods of any oscillatory motion. However, it has been demonstrated that the molecular dynamics potential gives rise to motion with a continuum of periods greater than or equal to 10 fs. Furthermore, the energy instability of impulse MTS methods becomes exponentially worse at larger multiples of the half-periods. This rules out the possibility that a fortuitously chosen assortment of impulse multiple time steps longer than 5 fs could yield stable trajectories. 

Two simulation methods—Monte Carlo and molecular dynamics—allow calculation of the density profile and pressure difference of Eq. III-44 across the vapor-liquid interface [64, 65]. In the former method, the initial system consists of N molecules in assumed positions. An intermolecule potential function is chosen, such as the Lennard-Jones potential, and the positions are randomly varied until the energy of the system is at a minimum. The resulting configuration is taken to be the equilibrium one. In the molecular dynamics approach, the N molecules are given initial positions and velocities and the equations of motion are solved to follow the ensuing collisions until the set shows constant time-average thermodynamic properties. Both methods are computer intensive yet widely used. 

Schinke R and Huber J R 1993 Photodissociation dynamics of polyatomic molecules. The relationship between potential energy surfaces and the breaking of molecular bonds J. Rhys. Chem. 97 3463... 

The summation of pair-wise potentials is a good approximation for molecular dynamics calculations for simple classical many-body problems [27], It has been widely used to simulate hyperthennal energy (>1 eV) atom-surface scattering ... 

Molecular dynamics consists of the brute-force solution of Newton s equations of motion. It is necessary to encode in the program the potential energy and force law of interaction between molecules the equations of motion are solved numerically, by finite difference techniques. The system evolution corresponds closely to what happens in real life and allows us to calculate dynamical properties, as well as thennodynamic and structural fiinctions. For a range of molecular models, packaged routines are available, either connnercially or tlirough the academic conmuinity. 

Hammes-Schiffer S and Tully J C 1995 Nonadiabatic transition state theory and multiple potential energy surfaces molecular dynamics of infrequent events J. Chem. Phys. 103 8528... 

Chemical reaction dynamics is an attempt to understand chemical reactions at tire level of individual quantum states. Much work has been done on isolated molecules in molecular beams, but it is unlikely tliat tliis infonnation can be used to understand condensed phase chemistry at tire same level [8]. In a batli, tire reacting solute s potential energy surface is altered by botli dynamic and static effects. The static effect is characterized by a potential of mean force. The dynamical effects are characterized by tire force-correlation fimction or tire frequency-dependent friction [8]. 

The stoi7 begins with studies of the molecular Jahn-Teller effect in the late 1950s [1-3]. The Jahn-Teller theorems themselves [4,5] are 20 years older and static Jahn-Teller distortions of elecbonically degenerate species were well known and understood. Geomebic phase is, however, a dynamic phenomenon, associated with nuclear motions in the vicinity of a so-called conical intersection between potential energy surfaces. 

The full dynamical treatment of electrons and nuclei together in a laboratory system of coordinates is computationally intensive and difficult. However, the availability of multiprocessor computers and detailed attention to the development of efficient software, such as ENDyne, which can be maintained and debugged continually when new features are added, make END a viable alternative among methods for the study of molecular processes. Eurthemiore, when the application of END is compared to the total effort of accurate determination of relevant potential energy surfaces and nonadiabatic coupling terms, faithful analytical fitting and interpolation of the common pointwise representation of surfaces and coupling terms, and the solution of the coupled dynamical equations in a suitable internal coordinates, the computational effort of END is competitive. 

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