期刊
JOURNAL OF COMPUTATIONAL CHEMISTRY
卷 30, 期 16, 页码 2706-2711出版社
WILEY-BLACKWELL
DOI: 10.1002/jcc.21296
关键词
molecular dynamics simulation; ab initio QM/MM method; time step; free energy profile; umbrella sampling
资金
- National Science Foundation [CHE-CAREER-0448156]
- National Institute of Health [R01-GM079223]
- NYSTAR
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 I 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. (C) 2009 Wiley Periodicals, Inc. J Comput Chem 30: 2706-2711, 2009
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