The previously developed particle mesh Ewald method is reformulated in terms of efficient B‐spline interpolation of the structure factors This reformulation allows a natural extension of the method to potentials of the form 1/rp with p≥1 Furthermore, efficient calculation of the virial tensor follows Use of B‐splines in place of Lagrange interpolation leads to analytic gradients as well as a significant improvement in the accuracy We demonstrate that arbitrary accuracy can be achieved, independent of system size N, at a cost that scales as N log(N) For biomolecular systems with many thousands of atoms this method permits the use of Ewald summation at a computational cost comparable to that of a simple truncation method of 10 A or less

A smooth particle mesh Ewald method

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and laptop computers. NAMD works with AMBER and CHARMM potential functions, parameters, and file formats. This article, directed to novices as well as experts, first introduces concepts and methods used in the NAMD program, describing the classical molecular dynamics force field, equations of motion, and integration methods along with the efficient electrostatics evaluation algorithms employed and temperature and pressure controls used. Features for steering the simulation across barriers and for calculating both alchemical and conformational free energy differences are presented. The motivations for and a roadmap to the internal design of NAMD, implemented in C++ and based on Charm++ parallel objects, are outlined. The factors affecting the serial and parallel performance of a simulation are discussed. Finally, typical NAMD use is illustrated with representative applications to a small, a medium, and a large biomolecular system, highlighting particular features of NAMD, for example, the Tcl scripting language. The article also provides a list of the key features of NAMD and discusses the benefits of combining NAMD with the molecular graphics/sequence analysis software VMD and the grid computing/collaboratory software BioCoRE. NAMD is distributed free of charge with source code at www.ks.uiuc.edu.

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Scalable molecular dynamics with NAMD

Molecular simulation is an extremely useful, but computationally very expensive tool for studies of chemical and biomolecular systems Here, we present a new implementation of our molecular simulation toolkit GROMACS which now both achieves extremely high performance on single processors from algorithmic optimizations and hand-coded routines and simultaneously scales very well on parallel machines The code encompasses a minimal-communication domain decomposition algorithm, full dynamic load balancing, a state-of-the-art parallel constraint solver, and efficient virtual site algorithms that allow removal of hydrogen atom degrees of freedom to enable integration time steps up to 5 fs for atomistic simulations also in parallel To improve the scaling properties of the common particle mesh Ewald electrostatics algorithms, we have in addition used a Multiple-Program, Multiple-Data approach, with separate node domains responsible for direct and reciprocal space interactions Not only does this combination of a

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GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation

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Scalable Molecular Dynamics with NAMD

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.

The relationship between DNA structure and function is fundamental to the understanding of biological processes. Currently, the most reliable source of biomolecular structural information comes from X-ray crystallographic data. Recent advances in theoretical modeling techniques have allowed molecular simulations to approach the accuracy obtainable from X-ray crystallography for proteins. We report the results of a 2.2 ns simulation of the B-DNA dodecamer d[CGCGAATTCGCG12 in a crystal unit cell, and demonstrate that, with rigorous accommodation of long-range forces, molecular simulation may be extended to provide atomic level accuracy of polynucleotide structures. Most of what is known about DNA structure has been derived from crystal structure analyses. A concern that has been expressed brings into question the degree to which the intrinsic structure of DNA is disrupted by the crystal lattice. It has been recently pointed out by Dickerson’ that lattice forces in DNA crystals are relatively weak, and that in fact these forces can be exploited to obtain useful information about DNA deformability. This notion strikes at the heart of a fundamental problem in structural biology: to understand the nature of DNA structure in the presence of environmental forces in vivo. A powerful theoretical technique for studying biomolecular structure is molecular simulation. The reliability of molecular simulation to the study of polynucleotide structure, however, has lagged behind that of proteins. This is largely because of the difficulty associated with accommodation of long-range electrostatic forces. In conventional macromolecular simulations, pairwise Coulomb interactions are evaluated using a finite cutoff to decrease computational effort. Ultimately, this truncation of the Coulomb potential leads to unrealistic behaviors2 The adverse effects of the cutoff methods are amplified in highly ionic systems such as DNA. In an attempt to circumvent these problems, artificial constructs are frequently introduced such as reduced phosphate charges on the nucleotide ba~kbone,~ modified Coulomb potentials in the form of distance dependent dielectric function^^,^ or switching function^,^,^ and distance restraints to enforce Watson-Crick hydrogen Perhaps the most studied DNA sequence both experimentally and theoretically is the dodecamer sequence d[CGCGAATTCGCG]2.8,9 Recent attempts to simulate the dodecamer in solution using full charges on the phosphates and explicit counterions to balance the charge led to structures that were

Toward the Accurate Modeling of DNA: The Importance of Long-Range Electrostatics

Accurate crystal molecular dynamics simulations using particle-mesh-Ewald: RNA dinucleotides — ApU and GpC

We report two 1 ns molecular dynamic (MD) simulations on Z‐DNA for which the long‐range Coulomb terms are explicitly evaluated by the Particle–Mesh–Ewald method [J. Chem. Phys. 98, 10089 (1993)]. The starting structures were based on the 1 A resolution crystallographic structure of Gessner et al. [J. Bio. Chem. 264, 7921 (1989)]. The average simulation structures of the DNA compare well to the crystallographic structure; the root‐mean‐square position deviations for the DNA double‐strand heavy atoms are approximately 0.5 A. Watson–Crick hydrogen bonding patterns are preserved without invoking constraints. These results emphasize the importance of proper treatment of the long‐range forces for highly ionic systems.

Hsing Lee

Papers

A smooth particle mesh Ewald method

Toward the Accurate Modeling of DNA: The Importance of Long-Range Electrostatics

Accurate crystal molecular dynamics simulations using particle-mesh-Ewald: RNA dinucleotides — ApU and GpC

Molecular dynamics simulation studies of a high resolution z-dna crystal