Increasing the time step with mass scaling in born-oppenheimer ab Initio QM/MM molecular dynamics simulations

Han Zheng, Shenglong Wang, Yingkai Zhang

Research output: Contribution to journalArticle

Abstract

Born-Oppenheimer ab initio QM/MM molecular dynamics simulation with umbrella sampling is a state-of-the-art approach to calculate free energy profiles of chemical reactions in complex systems. To further improve its computational efficiency, a mass-scaling method with the increased time step in MD simulations has been explored and tested. It is found that by increasing the hydrogen mass to 10 amu, a time step of 3 fs can be employed in ab initio QM/MM MD simulations. In all our three test cases, including two solution reactions and one enzyme reaction, the resulted reaction free energy profiles with 3 fs time step and mass scaling are found to be in excellent agreement with the corresponding simulation results using 1 fs time step and the normal mass. These results indicate that for Born-Oppenheimer ab initio QM/MM molecular dynamics simulations with umbrella sampling, the mass-scaling method can significantly reduce its computational cost while has little effect on the calculated free energy profiles.

Original languageEnglish (US)
Pages (from-to)2706-2711
Number of pages6
JournalJournal of Computational Chemistry
Volume30
Issue number16
DOIs
StatePublished - Dec 2009

Fingerprint

Molecular Dynamics Simulation
Free energy
Molecular dynamics
Scaling
MD Simulation
Computer simulation
Free Energy
Sampling
Computational efficiency
Large scale systems
Chemical reactions
Hydrogen
Enzymes
Chemical Reaction
Computational Efficiency
Computational Cost
Complex Systems
Costs
Calculate
Profile

Keywords

  • Ab initio QM/MM method
  • Free energy profile
  • Molecular dynamics simulation
  • Time step
  • Umbrella sampling

ASJC Scopus subject areas

  • Chemistry(all)
  • Computational Mathematics

Cite this

Increasing the time step with mass scaling in born-oppenheimer ab Initio QM/MM molecular dynamics simulations. / Zheng, Han; Wang, Shenglong; Zhang, Yingkai.

In: Journal of Computational Chemistry, Vol. 30, No. 16, 12.2009, p. 2706-2711.

Research output: Contribution to journalArticle

@article{049efe19d89b4fd5a39b717ab631ee88,
title = "Increasing the time step with mass scaling in born-oppenheimer ab Initio QM/MM molecular dynamics simulations",
abstract = "Born-Oppenheimer ab initio QM/MM molecular dynamics simulation with umbrella sampling is a state-of-the-art approach to calculate free energy profiles of chemical reactions in complex systems. To further improve its computational efficiency, a mass-scaling method with the increased time step in MD simulations has been explored and tested. It is found that by increasing the hydrogen mass to 10 amu, a time step of 3 fs can be employed in ab initio QM/MM MD simulations. In all our three test cases, including two solution reactions and one enzyme reaction, the resulted reaction free energy profiles with 3 fs time step and mass scaling are found to be in excellent agreement with the corresponding simulation results using 1 fs time step and the normal mass. These results indicate that for Born-Oppenheimer ab initio QM/MM molecular dynamics simulations with umbrella sampling, the mass-scaling method can significantly reduce its computational cost while has little effect on the calculated free energy profiles.",
keywords = "Ab initio QM/MM method, Free energy profile, Molecular dynamics simulation, Time step, Umbrella sampling",
author = "Han Zheng and Shenglong Wang and Yingkai Zhang",
year = "2009",
month = "12",
doi = "10.1002/jcc.21296",
language = "English (US)",
volume = "30",
pages = "2706--2711",
journal = "Journal of Computational Chemistry",
issn = "0192-8651",
publisher = "John Wiley and Sons Inc.",
number = "16",

}

TY - JOUR

T1 - Increasing the time step with mass scaling in born-oppenheimer ab Initio QM/MM molecular dynamics simulations

AU - Zheng, Han

AU - Wang, Shenglong

AU - Zhang, Yingkai

PY - 2009/12

Y1 - 2009/12

N2 - Born-Oppenheimer ab initio QM/MM molecular dynamics simulation with umbrella sampling is a state-of-the-art approach to calculate free energy profiles of chemical reactions in complex systems. To further improve its computational efficiency, a mass-scaling method with the increased time step in MD simulations has been explored and tested. It is found that by increasing the hydrogen mass to 10 amu, a time step of 3 fs can be employed in ab initio QM/MM MD simulations. In all our three test cases, including two solution reactions and one enzyme reaction, the resulted reaction free energy profiles with 3 fs time step and mass scaling are found to be in excellent agreement with the corresponding simulation results using 1 fs time step and the normal mass. These results indicate that for Born-Oppenheimer ab initio QM/MM molecular dynamics simulations with umbrella sampling, the mass-scaling method can significantly reduce its computational cost while has little effect on the calculated free energy profiles.

AB - Born-Oppenheimer ab initio QM/MM molecular dynamics simulation with umbrella sampling is a state-of-the-art approach to calculate free energy profiles of chemical reactions in complex systems. To further improve its computational efficiency, a mass-scaling method with the increased time step in MD simulations has been explored and tested. It is found that by increasing the hydrogen mass to 10 amu, a time step of 3 fs can be employed in ab initio QM/MM MD simulations. In all our three test cases, including two solution reactions and one enzyme reaction, the resulted reaction free energy profiles with 3 fs time step and mass scaling are found to be in excellent agreement with the corresponding simulation results using 1 fs time step and the normal mass. These results indicate that for Born-Oppenheimer ab initio QM/MM molecular dynamics simulations with umbrella sampling, the mass-scaling method can significantly reduce its computational cost while has little effect on the calculated free energy profiles.

KW - Ab initio QM/MM method

KW - Free energy profile

KW - Molecular dynamics simulation

KW - Time step

KW - Umbrella sampling

UR - http://www.scopus.com/inward/record.url?scp=70349895348&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=70349895348&partnerID=8YFLogxK

U2 - 10.1002/jcc.21296

DO - 10.1002/jcc.21296

M3 - Article

VL - 30

SP - 2706

EP - 2711

JO - Journal of Computational Chemistry

JF - Journal of Computational Chemistry

SN - 0192-8651

IS - 16

ER -