Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

6.2.2. Definition of Effective Properties 3064 6.3. Response Properties to Magnetic Fields 3066 6.3.1. Nuclear Shielding 3066 6.3.2. Indirect Spin−Spin Coupling 3067 6.3.3. EPR Parameters 3068 6.4. Properties of Chiral Systems 3069 6.4.1. Electronic Circular Dichroism (ECD) 3069 6.4.2. Optical Rotation (OR) 3069 6.4.3. VCD and VROA 3070 7. Continuum and Discrete Models 3071 7.1. Continuum Methods within MD and MC Simulations 3072

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Quantum mechanical continuum solvation models.

CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecu- lar simulation program. It has been developed over the last three decades with a primary focus on molecules of bio- logical interest, including proteins, peptides, lipids, nucleic acids, carbohydrates, and small molecule ligands, as they occur in solution, crystals, and membrane environments. For the study of such systems, the program provides a large suite of computational tools that include numerous conformational and path sampling methods, free energy estima- tors, molecular minimization, dynamics, and analysis techniques, and model-building capabilities. The CHARMM program is applicable to problems involving a much broader class of many-particle systems. Calculations with CHARMM can be performed using a number of different energy functions and models, from mixed quantum mechanical-molecular mechanical force fields, to all-atom classical potential energy functions with explicit solvent and various boundary conditions, to implicit solvent and membrane models. The program has been ported to numer- ous platforms in both serial and parallel architectures. This article provides an overview of the program as it exists today with an emphasis on developments since the publication of the original CHARMM article in 1983.

/pdf/charmm-the-biomolecular-simulation-program-4kexem0xkx.pdf

CHARMM: the biomolecular simulation program.

The calculation of rate coefficients is a discipline of nonlinear science of importance to much of physics, chemistry, engineering, and biology. Fifty years after Kramers' seminal paper on thermally activated barrier crossing, the authors report, extend, and interpret much of our current understanding relating to theories of noise-activated escape, for which many of the notable contributions are originating from the communities both of physics and of physical chemistry. Theoretical as well as numerical approaches are discussed for single- and many-dimensional metastable systems (including fields) in gases and condensed phases. The role of many-dimensional transition-state theory is contrasted with Kramers' reaction-rate theory for moderate-to-strong friction; the authors emphasize the physical situation and the close connection between unimolecular rate theory and Kramers' work for weakly damped systems. The rate theory accounting for memory friction is presented, together with a unifying theoretical approach which covers the whole regime of weak-to-moderate-to-strong friction on the same basis (turnover theory). The peculiarities of noise-activated escape in a variety of physically different metastable potential configurations is elucidated in terms of the mean-first-passage-time technique. Moreover, the role and the complexity of escape in driven systems exhibiting possibly multiple, metastable stationary nonequilibrium states is identified. At lower temperatures, quantum tunneling effects start to dominate the rate mechanism. The early quantum approaches as well as the latest quantum versions of Kramers' theory are discussed, thereby providing a description of dissipative escape events at all temperatures. In addition, an attempt is made to discuss prominent experimental work as it relates to Kramers' reaction-rate theory and to indicate the most important areas for future research in theory and experiment.

Reaction-rate theory: fifty years after Kramers

We introduce a powerful method for exploring the properties of the multidimensional free energy surfaces (FESs) of complex many-body systems by means of coarse-grained non-Markovian dynamics in the space defined by a few collective coordinates. A characteristic feature of these dynamics is the presence of a history-dependent potential term that, in time, fills the minima in the FES, allowing the efficient exploration and accurate determination of the FES as a function of the collective coordinates. We demonstrate the usefulness of this approach in the case of the dissociation of a NaCl molecule in water and in the study of the conformational changes of a dialanine in solution.

https://www.pnas.org/content/pnas/99/20/12562.full.pdf

Escaping free-energy minima

The time correlation function (tcf) formulas for rate constants κ derived via the stable states picture (SSP) of chemical reactions are applied to a wide variety (a–d) of gas and solution phase reactionmodels. (a) For gas phase bimolecular reactions, we show that the flux tcf governing κ corresponds to standard numerical trajectory calculation methods. Alternate formulas for κ are derived which focus on saddle point surfaces, thus increasing computational efficiency. Advantages of the SSP formulas for κ are discussed. (b) For gas phase unimolecular reactions, simple results for κ are found in both the strong and weak coupling collision limits; the often ignored role of product stabilization is exposed for reversible isomerizations. The SSP results correct some standard weak coupling rate constant results by as much as 50%. (c) For barrier crossing reactions in solution, we evaluate κ for a generalized (non‐Markovian) Langevin description of the dynamics. For several realistic models of time dependent friction, κ differs dramatically from the popular Kramers constant friction predictions; this has important implications for the validity of transition state theory. (d) For solutionreactions heavily influenced by spatial diffusion, we show that the SSP isolates short range reaction dynamics of interest and includes important barrier region effects in structural isomerizations often missed in standard descriptions.

The stable states picture of chemical reactions. II. Rate constants for condensed and gas phase reaction models

Despite long study, a molecular picture of the mechanism of water reorientation is still lacking Using numerical simulations, we find support for a pathway in which the rotating water molecule breaks a hydrogen bond (H-bond) with an overcoordinated first-shell neighbor to form an H-bond with an undercoordinated second-shell neighbor The H-bond cleavage and the molecular reorientation occur concertedly and not successively as usually considered This water reorientation mechanism involves large-amplitude angular jumps, rather than the commonly accepted sequence of small diffusive steps, and therefore calls for reinterpretation of many experimental data wherein water rotational relaxation is assumed to be diffusive

https://science.sciencemag.org/content/sci/311/5762/832.full.pdf

A molecular jump mechanism of water reorientation.

Constrained reaction coordinate dynamics for the simulation of rare events

The structure and function of biomolecules are strongly influenced by their hydration shells. Structural fluctuations and molecular excitations of hydrating water molecules cover a broad range in space and time, from individual water molecules to larger pools and from femtosecond to microsecond time scales. Recent progress in theory and molecular dynamics simulations as well as in ultrafast vibrational spectroscopy has led to new and detailed insight into fluctuations of water structure, elementary water motions, electric fields at hydrated biointerfaces, and processes of vibrational relaxation and energy dissipation. Here, we review recent advances in both theory and experiment, focusing on hydrated DNA, proteins, and phospholipids, and compare dynamics in the hydration shells to bulk water.

http://pubs.acs.org/doi/pdf/10.1021/acs.chemrev.6b00765

James T. Hynes

Papers

The stable states picture of chemical reactions. II. Rate constants for condensed and gas phase reaction models

A molecular jump mechanism of water reorientation.

Constrained reaction coordinate dynamics for the simulation of rare events

Water Dynamics in the Hydration Shells of Biomolecules

Time-dependent fluorescence solvent shifts, dielectric friction, and nonequilibrium solvation in polar solvents