### Abstract

A central goal in molecular dynamics simulations is increasing the integration time-step to allow the capturing of biomolecular motion on biochemically interesting time frames. We previously made a step in that direction by developing the Langevidimplicit-Euler scheme. Here, we present a modified Langevin/implicit-Euler formulation for molecular dynamics. The new method still maintains the major advantage of the original scheme, namely, stability over a wide range of time-steps. However, it substantially reduces the damping effect of the high-frequency modes inherent in the original implicit scheme. The new formulation involves separation of the solution into two components, one of which is solved exactly using normal-mode techniques, the other of which is solved by implicit numerical integration. In this way, the high-frequency and fast-varying components are well resolved in the analytic solution component, while the remaining components of the motion are obtained by a large time-step integration phase. Full details of the new scheme are presented, accompanied by illustrative examples for a simple pendulum system. An application to liquid butane dem- onstrates stability of the simulations at time-steps up to 50 fs, still with activation of the high-frequency modes.

Original language | English (US) |
---|---|

Pages (from-to) | 1212-1233 |

Number of pages | 22 |

Journal | Journal of Computational Chemistry |

Volume | 14 |

Issue number | 10 |

State | Published - Oct 1 1993 |

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### ASJC Scopus subject areas

- Chemistry(all)
- Computational Mathematics

### Cite this

**Lin : A new algorithm to simulate the dynamics of biomolecules by combining implicit-integration and normal mode techniques.** / Zhang, Guihua; Schlick, Tamar.

Research output: Contribution to journal › Article

*Journal of Computational Chemistry*, vol. 14, no. 10, pp. 1212-1233.

}

TY - JOUR

T1 - Lin

T2 - A new algorithm to simulate the dynamics of biomolecules by combining implicit-integration and normal mode techniques

AU - Zhang, Guihua

AU - Schlick, Tamar

PY - 1993/10/1

Y1 - 1993/10/1

N2 - A central goal in molecular dynamics simulations is increasing the integration time-step to allow the capturing of biomolecular motion on biochemically interesting time frames. We previously made a step in that direction by developing the Langevidimplicit-Euler scheme. Here, we present a modified Langevin/implicit-Euler formulation for molecular dynamics. The new method still maintains the major advantage of the original scheme, namely, stability over a wide range of time-steps. However, it substantially reduces the damping effect of the high-frequency modes inherent in the original implicit scheme. The new formulation involves separation of the solution into two components, one of which is solved exactly using normal-mode techniques, the other of which is solved by implicit numerical integration. In this way, the high-frequency and fast-varying components are well resolved in the analytic solution component, while the remaining components of the motion are obtained by a large time-step integration phase. Full details of the new scheme are presented, accompanied by illustrative examples for a simple pendulum system. An application to liquid butane dem- onstrates stability of the simulations at time-steps up to 50 fs, still with activation of the high-frequency modes.

AB - A central goal in molecular dynamics simulations is increasing the integration time-step to allow the capturing of biomolecular motion on biochemically interesting time frames. We previously made a step in that direction by developing the Langevidimplicit-Euler scheme. Here, we present a modified Langevin/implicit-Euler formulation for molecular dynamics. The new method still maintains the major advantage of the original scheme, namely, stability over a wide range of time-steps. However, it substantially reduces the damping effect of the high-frequency modes inherent in the original implicit scheme. The new formulation involves separation of the solution into two components, one of which is solved exactly using normal-mode techniques, the other of which is solved by implicit numerical integration. In this way, the high-frequency and fast-varying components are well resolved in the analytic solution component, while the remaining components of the motion are obtained by a large time-step integration phase. Full details of the new scheme are presented, accompanied by illustrative examples for a simple pendulum system. An application to liquid butane dem- onstrates stability of the simulations at time-steps up to 50 fs, still with activation of the high-frequency modes.

UR - http://www.scopus.com/inward/record.url?scp=84913583406&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84913583406&partnerID=8YFLogxK

M3 - Article

AN - SCOPUS:84913583406

VL - 14

SP - 1212

EP - 1233

JO - Journal of Computational Chemistry

JF - Journal of Computational Chemistry

SN - 0192-8651

IS - 10

ER -