引用本文:
【打印本页】   【HTML】   【下载PDF全文】   View/Add Comment  【EndNote】   【RefMan】   【BibTex】
过刊浏览    高级检索
本文已被:浏览 17次   下载 42  
分享到: 微信 更多
Free energy level correction by Monte Carlo resampling with the weighted histogram analysis method
Young Min Rhee
Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
Abstract:
Free energy calculations may provide vital information for studying various chemical and biological processes. Quantum mechanical methods are required to accurately describe interaction energies, but their computations are often too demanding for conformational sampling. As a remedy, level correction schemes that allow calculating high level free energies based on conformations from lower level simulations have been developed. Here, we present a variation of a Monte Carlo (MC) resampling approach in relation to the weighted histogram analysis method (WHAM). We show that our scheme can generate free energy surfaces that can practically converge to the exact one with sufficient sampling, and that it treats cases with insufficient sampling in a more stable manner than the conventional WHAM-based level correction scheme. It can also provide a guide for checking the uncertainty of the level-corrected surface and a well-defined criterion for deciding the extent of smoothing on the free energy surface for its visual improvement. We demonstrate these aspects by obtaining the free energy maps associated with the alanine dipeptide and proton transfer network of the KillerRed protein in explicit water, and exemplify that the MC resampled WHAM scheme can be a practical tool for producing free energy surfaces of realistic systems.
Key words:  Free energy, level correction, WHAM, Monte Carlo resampling
FundProject:
Free energy level correction by Monte Carlo resampling with the weighted histogram analysis method
Young Min Rhee
Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
摘要:
Free energy calculations may provide vital information for studying various chemical and biological processes. Quantum mechanical methods are required to accurately describe interaction energies, but their computations are often too demanding for conformational sampling. As a remedy, level correction schemes that allow calculating high level free energies based on conformations from lower level simulations have been developed. Here, we present a variation of a Monte Carlo (MC) resampling approach in relation to the weighted histogram analysis method (WHAM). We show that our scheme can generate free energy surfaces that can practically converge to the exact one with sufficient sampling, and that it treats cases with insufficient sampling in a more stable manner than the conventional WHAM-based level correction scheme. It can also provide a guide for checking the uncertainty of the level-corrected surface and a well-defined criterion for deciding the extent of smoothing on the free energy surface for its visual improvement. We demonstrate these aspects by obtaining the free energy maps associated with the alanine dipeptide and proton transfer network of the KillerRed protein in explicit water, and exemplify that the MC resampled WHAM scheme can be a practical tool for producing free energy surfaces of realistic systems.
关键词:  Free energy, level correction, WHAM, Monte Carlo resampling
DOI:
分类号: