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 technology is used to solve large or complex computational problems on distributed computational resources belonging to multiple organizations regardless of their geographical locations. In this paper, we introduce an integration of the SAFORAH geospatial data grid, provided by the Canadian Forest Service, and the computational grids, offered by the University of Victoria and National Research Council Canada, using Globus Toolkit 4 (GT-4) as a common grid middleware. New GT-4 services, such as an Integration Service (IS), a Metascheduler Service (MS) and a Registry Service (RS) were designed and implemented. MS is a broker used to schedule jobs on many distinct computational clusters at the project partner sites. The RS is used to track the availability of resources at these sites. IS allows the data grid and computational grids to work together, so that users are able not only to access geospatial data directly from the SAFORAH data grid but also to create virtual image products on the fly using the computational grids. The new system is a prime example of sharing data and computational resources and collaborating between different organization and research communities. We envisage that the results of our system would be valuable to other projects that wish to combine large-scale data management systems with computational resources.

Geospatial data grid with computational capability

This paper introduces the Universal Personal Numbering System (UPN), an application that works with a Personal Agent Mobility Management System (PAMMS) to manage multiple communications devices. It allows messages to reach the user on different phones or messaging devices using one single number. This paper includes details on the design of the UPN application and how it works with a UPN service adapter agent to notify non-telephone devices of incoming calls and await instructions from the user. Additionally, there is a description of the interface between the UPN application and a PC-based switch using the TAPI protocol.

Software Agents for Enhancing Messaging in a Universal Personal Numbering Service

Grid portals typically store user grid credentials in a credential repository. Credential repositories allow users to access Grid portals from any machine having a Web browser, but their usage requires several authentication steps. Current portals require users to explicitly go through these steps, thereby hindering their usability. In this paper we present intuitive and easy to use tools to manage certificates. We also describe the integration of Grid Security Infrastructure authentication into a Java-based SSH terminal tool. Based on these tools, we build an innovative portal authentication mechanism that enables transparent delegation of credentials between clients, grid portal and the credential repository.

Roger Impey

Papers

Geospatial data grid with computational capability

Software Agents for Enhancing Messaging in a Universal Personal Numbering Service

Seamless and secure authentication for grid portals