Increasing the time step with mass scaling in Born-Oppenheimer ab initio QM/MM molecular dynamics simulations
✍ Scribed by Han Zheng; Shenglong Wang; Yingkai Zhang
- Publisher
- John Wiley and Sons
- Year
- 2009
- Tongue
- English
- Weight
- 290 KB
- Volume
- 30
- Category
- Article
- ISSN
- 0192-8651
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✦ Synopsis
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. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009