Topic
Shake
About: Shake is a research topic. Over the lifetime, 2204 publications have been published within this topic receiving 23595 citations.
Papers published on a yearly basis
1 / 2
Papers
TL;DR: In this article, an analytical algorithm called SETTLE for resetting the positions and velocities to satisfy the holonomic constraints on the rigid water model is presented, which is based on the Cartesian coordinate system and can be used in place of SHAKE and RATTLE.
Abstract: An analytical algorithm, called SETTLE, for resetting the positions and velocities to satisfy the holonomic constraints on the rigid water model is presented. This method is still based on the Cartesian coordinate system and can be used in place of SHAKE and RATTLE. We implemented this algorithm in the SPASMS package of molecular mechanics and dynamics. Several series of molecular dynamics simulations were carried out to examine the performance of the new algorithm in comparison with the original RATTLE method. It was found that SETTLE is of higher accuracy and is faster than RATTLE with reasonable tolerances by three to nine times on a scalar machine. Furthermore, the performance improvement ranged from factors of 26 to 98 on a vector machine since the method presented is not iterative. © 1992 by John Wiley & Sons, Inc.
7,189 citations
TL;DR: In this paper, an algorithm, called RATTLE, for integrating the equations of motion in molecular dynamics calculations for molecular models with internal constraints is presented. But it is based on the Verlet algorithm and retains the simplicity of using Cartesian coordinates for each of the atoms to describe the configuration of a molecule with internal constraint.
3,094 citations
1 Jan 1972
1,638 citations
TL;DR: In this paper, an alternative method, M-SHAKE, which solves the coupled equations simultaneously by matrix inversion, was proposed and compared in simulations of the pure solvents water, dimethyl sulfoxide, and chloroform.
Abstract: A common method for the application of distance constraints in molecular simulations employing Cartesian coordinates is the SHAKE procedure for determining the Lagrange multipliers regarding the constraints. This method relies on the linearization and decoupling of the equations governing the atomic coordinate resetting corresponding to each constraint in a molecule, and is thus iterative. In the present study, we consider an alternative method, M-SHAKE, which solves the coupled equations simultaneously by matrix inversion. The performances of the two methods are compared in simulations of the pure solvents water, dimethyl sulfoxide, and chloroform. It is concluded that M-SHAKE is significantly faster than SHAKE when either (1) the molecules contain few distance constraints (solvent), or (2) when a high level of accuracy is required in the application of the constraints. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 501–508, 2001
1,215 citations
1 Jan 1970
TL;DR: Educational apparatus with a circuitry board provided to receive a program pannel having a problem or question section and response or answer section to permit the operator to first, through contact engaging means, select a question in the question section to be answered, and, secondly, seek proper selection of an answer in the answer section, the correct response being indicated by signal means, such as, in the form of a light or bell.
934 citations
Related Topics (5)
Performance Metrics
| Year | Papers |
|---|---|
| 2025 | 96 |
| 2024 | 152 |
| 2023 | 128 |
| 2022 | 146 |
| 2021 | 28 |
| 2020 | 59 |