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

Infrared spectroscopy of proteins.

1. Introduction 46372. Theoretical Methodologies and Simulation Tools 46402.1. Ab Initio Quantum Chemistry 46412.2. Molecular Dynamics 46422.2.1. Classical Molecular Dynamics and MonteCarlo Simulations46432.2.2. Empirical Valence Bond Models 46442.2.3. Ab Initio Molecular Dynamics (AIMD) 46452.3. Poisson−Boltzmann Theory 46452.4. Nonequilibrium Statistical Mechanical IonTransport Modeling46462.5. Dielectric Saturation 46473. Transport Mechanisms 46483.1. Proton Conduction Mechanisms 46483.1.1. Homogeneous Media 46483.1.2. Heterogeneous Systems (ConfinementEffects)46553.2. Mechanisms of Parasitic Transport 46613.2.1. Solvated Acidic Polymers 46613.2.2. Oxides 46654. Phenomenology of Transport inProton-Conducting Materials for Fuel-CellApplications46664.1. Hydrated Acidic Polymers 46664.2. PBI−H

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Transport in proton conductors for fuel-cell applications: simulations, elementary reactions, and phenomenology.

This article reviews the concepts and methods of transition path sampling. These methods allow computational studies of rare events without requiring prior knowledge of mechanisms, reaction coordinates, and transition states. Based upon a statistical mechanics of trajectory space, they provide a perspective with which time dependent phenomena, even for systems driven far from equilibrium, can be examined with the same types of importance sampling tools that in the past have been applied so successfully to static equilibrium properties.

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TRANSITION PATH SAMPLING: Throwing Ropes Over Rough Mountain Passes, in the Dark

When Szent-Gyorgyi called water the “matrix of life”,1 he was echoing an old sentiment. Paracelsus in the 16th century said that “water was the matrix of the world and of all its creatures.”2 But Paracelsus’s notion of a matrixsan active substance imbued with fecund, life-giving propertiess was quite different from the picture that, until very recently, molecular biologists have tended to hold of water’s role in the chemistry of life. Although acknowledging that liquid water has some unusual and important physical and chemical propertiessits potency as a solvent, its ability to form hydrogen bonds, its amphoteric naturesbiologists have regarded it essentially as the backdrop on which life’s molecular components are arrayed. It used to be common practice, for example, to perform computer simulations of biomolecules in a vacuum. Partly this was because the computational intensity of simulating a polypeptide chain was challenging even without accounting for solvent molecules too, but it also reflected the prevailing notion that water does little more than temper or moderate the basic physicochemical interactions responsible for molecular biology. What Gerstein and Levitt said 9 years ago remains true today: “When scientists publish models of biological molecules in journals, they usually draw their models in bright colors and place them against a plain, black background”.3 Curiously, this neglect of water as an active component of the cell went hand in hand with the assumption that life could not exist without it. That was basically an empirical conclusion derived from our experience of life on Earth: environments without liquid water cannot sustain life, and special strategies are needed to cope with situations in which, because of extremes of either heat or cold, the liquid is scarce.4-6 The recent confirmation that there is at least one world rich in organic molecules on which rivers and perhaps shallow seas or bogs are filled with nonaqueous fluidsthe liquid hydrocarbons of Titan7smight now bring some focus, even urgency, to the question of whether water is indeed a * E-mail: p.ball@nature.com. Philip Ball is a science writer and a consultant editor for Nature, where he worked as an editor for physical sciences for more than 10 years. He holds a Ph.D. in physics from the University of Bristol, where he worked on the statistical mechanics of phase transitions in the liquid state. His book H2O: A Biography of Water (Weidenfeld & Nicolson, 1999) was a survey of the current state of knowledge about the behavior of water in situations ranging from planetary geomorphology to cell biology. He frequently writes about aspects of water science for both the popular and the technical media.

https://www.philipball.co.uk/images/stories/docs/pdf/ChemRev_final.pdf

Water as an Active Constituent in Cell Biology

The dynamics and energetics of an excess proton in bulk phase water are examined computationally with a special emphasis on a quantum-dynamical treatment of the nuclear motion. The potential model used, the recently developed multistate empirical valence bond (MS-EVB) approach [U. W. Schmitt and G. A. Voth, J. Phys. Chem. B 102, 5547 (1998)], is also further refined and described in more detail. The MS-EVB model takes into account the interaction of an exchange charge distribution of the charge-transfer complex with the polar solvent, which qualitatively changes the nature of the solvated complex. Classical and quantum molecular dynamics simulations of the excess proton in bulk phase water reveal that quantization of the nuclear degrees of freedom results in an increased stabilization of the solvated H5O2+ (Zundel) cation relative to the H9O4+ (Eigen) cation, though the latter is still more stable, and that a species intermediate between the two also exists. The quantum proton transport rate, which is eva...

The computer simulation of proton transport in water

Building on the previously developed multistate empirical valence bond model [U. W. Schmitt and G. A. Voth, J. Chem. Phys 111, 9361 (1999)] for the dynamics and energetics of an excess proton in bulk phase water, a second generation model is described. This model is shown to produce similar dynamic and structural properties to the previous model, while allowing for the use of the full hydronium charge. This characteristic of the model is required for its implementation in a host of realistic applications beyond bulk water. An improved state selection algorithm is also presented, resulting in a significantly reduced energy drift during microcanonical molecular dynamics simulations. The unusually high self diffusion constant of an excess proton in water due to the proton hopping (Grotthuss) process is observed in the simulation data and is found to be quantitatively in the same range as the experimental value if a quantum correction is taken into consideration. Importantly, a more complete analysis of proto...

A second generation multistate empirical valence bond model for proton transport in aqueous systems

The vibrational properties of the hydrated proton and deuteron in bulk phase water and deuterated water are investigated spectroscopically and computationally. Mid-infrared spectra of aqueous acid solutions are measured by attenuated total reflectance-Fourier transform IR spectroscopy and compared with pure water and salt/counterion spectra to extract high-quality hydrated proton spectra at a series of concentrations. Multistate empirical valence bond simulations of the excess proton in bulk phase water are also performed, allowing the autocorrelation function of the time derivative of the dipole moment, and hence the power spectrum of the hydrated proton, to be evaluated. The experimental and theoretical spectra are found to be in very good agreement. Normal mode analysis of the bulk phase simulation data allows definitive assignment of the spectrum. The associated motions are found to be represented by both Eigen and Zundel forms of the hydrated proton.

The vibrational spectrum of the hydrated proton: Comparison of experiment, simulation, and normal mode analysis

The formation and dynamics of proton wires in channel environments.

We investigate the parallel scaling of the GROMACS molecular dynamics code on Ethernet Beowulf clusters and what prerequisites are necessary for decent scaling even on such clusters with only limited bandwidth and high latency. GROMACS 3.3 scales well on supercomputers like the IBM p690 (Regatta) and on Linux clusters with a special interconnect like Myrinet or Infiniband. Because of the high single-node performance of GROMACS, however, on the widely used Ethernet switched clusters, the scaling typically breaks down when more than two computer nodes are involved, limiting the absolute speedup that can be gained to about 3 relative to a single-CPU run. With the LAM MPI implementation, the main scaling bottleneck is here identified to be the all-to-all communication which is required every time step. During such an all-to-all communication step, a huge amount of messages floods the network, and as a result many TCP packets are lost. We show that Ethernet flow control prevents network congestion and leads to substantial scaling improvements. For 16 CPUs, e.g., a speedup of 11 has been achieved. However, for more nodes this mechanism also fails. Having optimized an all-to-all routine, which sends the data in an ordered fashion, we show that it is possible to completely prevent packet loss for any number of multi-CPU nodes. Thus, the GROMACS scaling dramatically improves, even for switches that lack flow control. In addition, for the common HP ProCurve 2848 switch we find that for optimum all-to-all performance it is essential how the nodes are connected to the switch's ports. This is also demonstrated for the example of the Car-Parinello MD code.

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Udo W. Schmitt

Papers

The computer simulation of proton transport in water

A second generation multistate empirical valence bond model for proton transport in aqueous systems

The vibrational spectrum of the hydrated proton: Comparison of experiment, simulation, and normal mode analysis

The formation and dynamics of proton wires in channel environments.

Speeding up parallel GROMACS on high-latency networks