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

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

Three recently proposed constant temperature molecular dynamics methods by: (i) Nose (Mol. Phys., to be published); (ii) Hoover et al. [Phys. Rev. Lett. 48, 1818 (1982)], and Evans and Morriss [Chem. Phys. 77, 63 (1983)]; and (iii) Haile and Gupta [J. Chem. Phys. 79, 3067 (1983)] are examined analytically via calculating the equilibrium distribution functions and comparing them with that of the canonical ensemble. Except for effects due to momentum and angular momentum conservation, method (1) yields the rigorous canonical distribution in both momentum and coordinate space. Method (2) can be made rigorous in coordinate space, and can be derived from method (1) by imposing a specific constraint. Method (3) is not rigorous and gives a deviation of order N−1/2 from the canonical distribution (N the number of particles). The results for the constant temperature–constant pressure ensemble are similar to the canonical ensemble case.

/pdf/a-unified-formulation-of-the-constant-temperature-molecular-dn26c8wsl1.pdf

A unified formulation of the constant temperature molecular dynamics methods

New protein parameters are reported for the all-atom empirical energy function in the CHARMM program. The parameter evaluation was based on a self-consistent approach designed to achieve a balance between the internal (bonding) and interaction (nonbonding) terms of the force field and among the solvent−solvent, solvent−solute, and solute−solute interactions. Optimization of the internal parameters used experimental gas-phase geometries, vibrational spectra, and torsional energy surfaces supplemented with ab initio results. The peptide backbone bonding parameters were optimized with respect to data for N-methylacetamide and the alanine dipeptide. The interaction parameters, particularly the atomic charges, were determined by fitting ab initio interaction energies and geometries of complexes between water and model compounds that represented the backbone and the various side chains. In addition, dipole moments, experimental heats and free energies of vaporization, solvation and sublimation, molecular volume...

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All-atom empirical potential for molecular modeling and dynamics studies of proteins.

This article describes the software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s. The software, written in ANSI C, originates from a parallel hardware project, and is well suited for parallelization on processor clusters. By careful optimization of neighbor searching and of inner loop performance, GROMACS is a very fast program for molecular dynamics simulation. It does not have a force field of its own, but is compatible with GROMOS, OPLS, AMBER, and ENCAD force fields. In addition, it can handle polarizable shell models and flexible constraints. The program is versatile, as force routines can be added by the user, tabulated functions can be specified, and analyses can be easily customized. Nonequilibrium dynamics and free energy determinations are incorporated. Interfaces with popular quantum-chemical packages (MOPAC, GAMES-UK, GAUSSIAN) are provided to perform mixed MM/QM simulations. The package includes about 100 utility and analysis programs. GROMACS is in the public domain and distributed (with source code and documentation) under the GNU General Public License. It is maintained by a group of developers from the Universities of Groningen, Uppsala, and Stockholm, and the Max Planck Institute for Polymer Research in Mainz. Its Web site is http://www.gromacs.org.

/pdf/gromacs-fast-flexible-and-free-15aazpel5u.pdf

GROMACS: Fast, flexible, and free

Grid computing supports sharing of distributed resources across boundaries and authorization domains, and can help scientists by providing secure, transparent and easy access to computing resources. We have designed and developed grid-based services for accessing, visualizing, and reliably manipulating remote spectrometry instruments. We harness grid-computing technologies to allow scientists to concentrate on performing experiments and data analysis, without having to become experts in the software technologies enabling these activities.

Remote services of spectroscopy instruments using grid computing

The present paper highlights the approach used to design and implement a web services based BaBar Monte Carlo (MC) production grid using Globus Toolkit version 4. The grid integrates the resources of two clusters at the University of Victoria, using the ClassAd mechanism provided by the Condor-G metascheduler. Each cluster uses the Portable Batch System (PBS) as its local resource management system (LRMS). Resource brokering is provided by the Condor matchmaking process, whereby the job and resource attributes are expressed as ClassAds. The important features of the grid are automatic registering of resource ClassAds to the central registry, ClassAds extraction from the registry to the metascheduler for matchmaking, and the incorporation of input/output file staging. Web-based monitoring is employed to track the status of grid resources and the jobs for an efficient operation of the grid. The performance of this new grid for BaBar jobs, and the existing Canadian computational grid (GridX1) based on Globus Toolkit version 2 is found to be consistent.

BaBar MC production on the Canadian grid using a web services approach

This paper proposes an agent-based service provisioning system for mobile users. It features a set of cooperative agents distributed over different sites that work together to provide personalized services for users within a mobile computing environment. For instance, when a user moves outside of his office, he would like to have a similar office environment while he is at home, in a meeting at another company, on a business trip or at a temporary location such as a hotel. Agents representing the end-users and the system agents may engage into a negotiation process to help the user access personalized services at particular site in accordance with the user's home policies and his current location policies. Adaptive Service Presentation agent is used to adapt the service presentation to the capabilities of the user's device (e.g. Workstation, Laptop, Phone, PDA). This work is part of the Mobile Agent Alliance project involving University of Ottawa, National Research Council and Mitel Corporation in Canada.

Agent-based personalized services in a mobile computing environment

Ionic Solvation in Nonaqueous Solvents: The Structure of Li+ and Cl- in Methanol, Ammonia, and Methylamine

The SAFORAH project (System of Agents for Forest Observation Research with Advanced Hierarchies) was created to coordinate and streamline the archiving and sharing of large geospatial data sets between various research groups within the Canadian Forest Service, the University of Victoria, and various other academic and government partners. Recently, it has become apparent that the availability of image processing services would improve the utility of the SAFORAH system. We describe a project to integrate SAFORAH with a computational grid using the Globus middleware. We outline a modular design that will allow us to incorporate new components as well as enhance the long-term sustainability of the project. We will describe the status of this project showing how it will add a new capability to the SAFORAH forestry project giving researchers a powerful tool for environmental and forestry research.

Roger Impey

Papers

Remote services of spectroscopy instruments using grid computing

BaBar MC production on the Canadian grid using a web services approach

Agent-based personalized services in a mobile computing environment

Ionic Solvation in Nonaqueous Solvents: The Structure of Li+ and Cl- in Methanol, Ammonia, and Methylamine

Service-oriented grid computing for SAFORAH