Literature DB >> 16438570

On the calculation of time correlation functions by potential scaling.

Chenyue Xing1, Ioan Andricioaei.   

Abstract

We present and analyze a general method to calculate time correlation functions from molecular dynamics on scaled potentials for complex systems for which simulation is affected by broken ergodicity. Depending on the value of the scaling factor, correlations can be calculated for times that can be orders of magnitude longer than those accessible to direct simulations. We show that the exact value of the time correlation functions of the original system (i.e., with unscaled potential) can be obtained, in principle, using an action-reweighting scheme based on a stochastic path-integral formalism. Two tests (involving a bistable potential model and a dipeptide bond-vector orientational relaxation) are exemplified to showcase the strengths, as well as the limitations of the approach, and a procedure for the estimation of the time-dependent standard deviation error is outlined.

Entities:  

Year:  2006        PMID: 16438570     DOI: 10.1063/1.2159476

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  3 in total

1.  Referencing strategy for the direct comparison of nuclear magnetic resonance and molecular dynamics motional parameters in RNA.

Authors:  Catherine Musselman; Qi Zhang; Hashim Al-Hashimi; Ioan Andricioaei
Journal:  J Phys Chem B       Date:  2010-01-21       Impact factor: 2.991

2.  Advances in milestoning. II. Calculating time-correlation functions from milestoning using stochastic path integrals.

Authors:  Gianmarc Grazioli; Ioan Andricioaei
Journal:  J Chem Phys       Date:  2018-08-28       Impact factor: 4.304

3.  Coupling Accelerated Molecular Dynamics Methods with Thermodynamic Integration Simulations.

Authors:  César Augusto F de Oliveira; Donald Hamelberg; J Andrew McCammon
Journal:  J Chem Theory Comput       Date:  2008-08-13       Impact factor: 6.006

  3 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.