Results 11 - 20 of 26,390

UCSF Chimera—a visualization system for exploratory research and analysis

by Eric F. Pettersen, Thomas D. Goddard, Conrad C. Huang, Gregory S. Couch, Daniel M. Greenblatt, Elaine C. Meng, Thomas E. Ferrin - J. Comput. Chem , 2004
"... Abstract: 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 ..."
Abstract - Cited by 504 (7 self) - Add to MetaCart
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

Scalable molecular dynamics with NAMD.

by James C Phillips , Rosemary Braun , Wei Wang , James Gumbart , Emad Tajkhorshid , Elizabeth Villa , Christophe Chipot , Robert D Skeel , Laxmikant Kalé , Klaus Schulten - J Comput Chem , 2005
"... Abstract: 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 la ..."
Abstract - Cited by 849 (63 self) - Add to MetaCart
Abstract: 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

TE: Clustering molecular dynamics trajectories: 1. Characterizing the Performance of different clustering algorithms

by Jianyin Shao, Stephen W. Tanner, Nephi Thompson, Thomas E. Cheatham - J Chem Theory Comput
"... Abstract: Molecular dynamics simulation methods produce trajectories of atomic positions (and optionally velocities and energies) as a function of time and provide a representation of the sampling of a given molecule’s energetically accessible conformational ensemble. As simulations on the 10-100 ns ..."
Abstract - Cited by 33 (1 self) - Add to MetaCart
Abstract: Molecular dynamics simulation methods produce trajectories of atomic positions (and optionally velocities and energies) as a function of time and provide a representation of the sampling of a given molecule’s energetically accessible conformational ensemble. As simulations on the 10

Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

by Jean-paul Ryckaert, Giovanni Ciccotti, Herman J. C. Berendsen - J. Comput. Phys , 1977
"... A numerical algorithm integrating the 3N Cartesian equations of motion of a system of N points subject to holonomic constraints is formulated. The relations of constraint remain perfectly fulfilled at each step of the trajectory despite the approximate character of numerical integration. The method ..."
Abstract - Cited by 704 (6 self) - Add to MetaCart
is applied to a molecular dynamics simulation of a liquid of 64 n-butane molecules and compared to a simulation using generalized coordinates. The method should be useful for molecular dynamics calculations on large molecules with internal degrees of freedom. 1. INTR~D~JCTI~N The method of molecular dynamics

Fast Parallel Algorithms for Short-Range Molecular Dynamics

by Steve Plimpton - JOURNAL OF COMPUTATIONAL PHYSICS , 1995
"... 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 dyn ..."
Abstract - Cited by 653 (7 self) - Add to MetaCart
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

Article pubs.acs.org/JCTC Efficient Construction of Mesostate Networks from Molecular Dynamics Trajectories

by Andreas Vitalis, Amedeo Caflisch
"... ABSTRACT: The coarse-graining of data from molecular simulations yields conformational space networks that may be used for predicting the system’s long time scale behavior, to discover structural pathways connecting free energy basins in the system, or simply to represent accessible phase space regi ..."
Abstract - Add to MetaCart
and barriers by which the system is characterized. Clustering or coarse-graining of molecular simulation data through measures of geometrical or kinetic similarity is a special case of a broad class of problems in data analysis. 1 Clustering of molecular trajectory information is used most often to identify

pubs.acs.org/JPCL Method to Predict Crowding Effects by Postprocessing Molecular Dynamics Trajectories: Application to the Flap

by Dynamics Of Hiv- Protease, Sanbo Qin, David D. L. Minh, J. Andrew Mccammon, Huan-xiang Zhou
"... ABSTRACT The internal dynamics of proteins inside of cells may be affected by the crowded intracellular environments. Here, we test a novel approach to simulations of crowding, in which simulations in the absence of crowders are postprocessed to predict crowding effects, against the direct approach ..."
Abstract - Add to MetaCart
ABSTRACT The internal dynamics of proteins inside of cells may be affected by the crowded intracellular environments. Here, we test a novel approach to simulations of crowding, in which simulations in the absence of crowders are postprocessed to predict crowding effects, against the direct approach

RESEARCH ARTICLE An Effective Approach for Clustering InhA Molecular Dynamics Trajectory Using Substrate-Binding Cavity Features

by Renata De Paris, Christian V. Quevedo, Duncan D. A. Ruiz, Osmar Norberto De
"... ☯ These authors contributed equally to this work. ..."
Abstract - Add to MetaCart
☯ These authors contributed equally to this work.

Randomized kinodynamic planning

by Steven M. Lavalle, James J. Kuffner, Jr. - THE INTERNATIONAL JOURNAL OF ROBOTICS RESEARCH 2001; 20; 378 , 2001
"... This paper presents the first randomized approach to kinodynamic planning (also known as trajectory planning or trajectory design). The task is to determine control inputs to drive a robot from an initial configuration and velocity to a goal configuration and velocity while obeying physically based ..."
Abstract - Cited by 626 (35 self) - Add to MetaCart
This paper presents the first randomized approach to kinodynamic planning (also known as trajectory planning or trajectory design). The task is to determine control inputs to drive a robot from an initial configuration and velocity to a goal configuration and velocity while obeying physically based

The Coordination of Arm Movements: An Experimentally Confirmed Mathematical Model

by Tamar Flash, Neville Hogans - Journal of neuroscience , 1985
"... This paper presents studies of the coordination of volun-tary human arm movements. A mathematical model is for-mulated which is shown to predict both the qualitative fea-tures and the quantitative details observed experimentally in planar, multijoint arm movements. Coordination is modeled mathematic ..."
Abstract - Cited by 688 (18 self) - Add to MetaCart
mathematically by defining an objective function, a measure of performance for any possi-ble movement. The unique trajectory which yields the best performance is determined using dynamic optimization the-ory. In the work presented here, the objective function is the square of the magnitude of jerk (rate
Results 11 - 20 of 26,390