The design, implementation, and capabilities of an extensible visualization system, UCSF Chimera, are discussed. Chimera is segmented into a core that provides basic services and visualization, and extensions that provide most higher level functionality. This architecture ensures that the extension mechanism satisfies the demands of outside developers who wish to incorporate new features. Two unusual extensions are presented: Multiscale, which adds the ability to visualize large-scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera session interactively despite being at separate locales. Other extensions include Multalign Viewer, for showing multiple sequence alignments and associated structures; ViewDock, for screening docked ligand orientations; Movie, for replaying molecular dynamics trajectories; and Volume Viewer, for display and analysis of volumetric data. A discussion of the usage of Chimera in real-world situations is given, along with anticipated future directions. Chimera includes full user documentation, is free to academic and nonprofit users, and is available for Microsoft Windows, Linux, Apple Mac OS X, SGI IRIX, and HP Tru64 Unix from http://www.cgl.ucsf.edu/chimera/.

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UCSF Chimera--a visualization system for exploratory research and analysis.

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

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

The continued-fraction formalism demonstrates that the Laplace-transformed dynamical correlations can be expressed as infinite continued fractions (ICF's). We propose a generalization of the dynamical convergence method (GDCM) of J. Hong and M. H. Lee [Phys. Rev. Lett. 55, 2375 (1985)] of perturbatively evaluating insoluble ICF's when a closely related ICF is exactly soluble. The proposed method overcomes an existing limitation of the dynamical convergence method which involves accurate computing of ratios of small numbers. The limitations are surmounted by exploiting an ``inversion'' property of ICF's. The GDCM allows computationally fast and simple perturbative evaluation of insoluble ICF's with up to ${10}^{\ensuremath{\xi}}$, \ensuremath{\xi}\ensuremath{\le}6, levels of the insoluble ICF when a related ICF is soluble. The method appears to be appropriate for studies of asymptotic behavior of dynamical correlations described by slowly converging and nonconverging ICF's, which are otherwise insoluble, when closely related soluble ICF's exist. The desirable feature of the GDCM is that the computation times required to solve the ICF's are unrelated to the details of the convergence properties. The method has been applied to recalculate the dynamical-spin pair correlation of a recently studied classical XX spin cluster. This application is described in this work.

Asymptotic behavior of dynamical correlations via perturbative analysis of infinite continued fractions.

We present a detailed report [see S. Sen {ital et al.}, Phys. Rev. Lett. {bold 77}, 4855 (1996)] of our {ital numerical} and {ital analytical} studies on the relaxation of a classical particle in the potentials V(x)={plus_minus}x{sup 2}/2+x{sup 4}/4. Both of the approaches confirm that at all temperatures, the relaxation functions (e.g., velocity relaxation function and position relaxation function) decay asymptotically in time {ital t} as sin({omega}{sub 0}t)/t. Numerically calculated power spectra of the relaxation functions show a gradual transition with increasing temperature from a single sharp peak located at the harmonic frequency {omega}{sub 0} to a broad continuous band. The 1/t relaxation is also found when V(x) is a polynomial in powers of x{sup 2} with a nonvanishing coefficient accompanying the x{sup 4} term in V(x). Numerical calculations show that in the cases in which the leading term in V(x) behaves as x{sup 2n} with integer {ital n}, the asymptotic relaxation exhibits 1/t{sup {phi}} decay where {phi}=1/(n{minus}1). We briefly discuss the analytical approaches to relaxation studies in these strongly anharmonic systems using direct solution of the equation of motion and using the continued fraction formalism approach for relaxation studies. We show that the study of the dynamics of stronglymore » anharmonic oscillators poses unique difficulties when studied via the continued fraction or any other time-series construction based approaches. We close with comments on the physical processes in which the insights presented in this work may be applicable. {copyright} {ital 1999} {ital The American Physical Society}« less

Slow algebraic relaxation in quartic potentials and related results.

Correction to Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems.

We consider the case of a chemically active AFM tip experiencing a bistable potential near a substrate while being driven by a periodic force of frequency Ω. The average position of such a tip traces a hysteretic loop which encircles an area π (Ω), which can reveal information on the tip-substrate interaction and on tip friction. We model this situation via a Smoluchowski diffusion equation and provide numerical results as well as construct asymptotic expansions for (Ω) in the limits of high and low frequency.

Modeling afm tip dynamics through diffusion in time-periodic potentials

While the Cell processor, jointly developed by IBM, Sony, and Toshiba, has great computational power, it also presents many challenges including portability and ease of programming. We have been adapting the Charm++ Runtime System to utilize the Cell. We believe that the Charm++ model fits well with the Cell for many reasons: encapsulation of data, effective prefetching, the ability to peak ahead in message queues, virtualization, etc. To these ends, we have developed the Offload API (an independent code) which allows Charm++ applications to easily take advantage of the Cell. Our goal is to allow Charm++ programs to run on Cell-based and non-Cell-based platforms without modification to application code. Example Charm++ programs using the Offload API already exist. We have also begun modifying NAMD, a popular molecular dynamics code, to use the Cell. In this poster, we plan to present current progress and future plans for this work.

James C. Phillips

Papers

Asymptotic behavior of dynamical correlations via perturbative analysis of infinite continued fractions.

Slow algebraic relaxation in quartic potentials and related results.

Correction to Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems.

Modeling afm tip dynamics through diffusion in time-periodic potentials

Charm++ simplifies coding for the cell processor