引用本文:
【打印本页】   【HTML】   【下载PDF全文】   View/Add Comment  【EndNote】   【RefMan】   【BibTex】
←前一篇|后一篇→ 过刊浏览    高级检索
本文已被:浏览 86次   下载 50 本文二维码信息
码上扫一扫!
分享到: 微信 更多
Free Energy Level Correction by Monte Carlo Resampling with Weighted Histogram Analysis Method
Seyoung Chung1, Sun Mi Choi1, Wook Lee1, Kwang Hyun Cho2, Young Min Rhee*2
1.Department of Chemistry, Pohang University of Science and Technology, Pohang 37673, Korea;2.Department of Chemistry, Korea Advanced Institute of Science and Technology, 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 levelcorrected 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, Weighted histogram analysis method, Monte Carlo resampling
FundProject:
Supplymentary:   CJCP2001001SP.pdf
采用加权直方图分析和蒙特卡洛重采样法对自由能级的校正研究
Seyoung Chung1, Sun Mi Choi1, Wook Lee1, Kwang Hyun Cho2, Young Min Rhee*2
1.韩国浦项科技大学化学系,浦项 37673;2.韩国高等科学技术学院校化学系,大田 34141
摘要:
本文采用加权直方图分析方法和蒙特卡洛重采样方法进行自由基校正研究. 生成的自由能表面几乎可以收敛到具有足够采样情况的精准表面,并且比常规的加权直方图分析校正方法能更稳定地处理采样不足的情况,为检测能级校正表面的不确定性提供指南,并且定义了明确的标准用以确定能改善其视觉效果的自由能表面平滑程度. 本文通过水中的丙氨酸二肽和KillerRed蛋白质子转移的自由能图证明该方法的优势,说明蒙特卡洛重采样法可以作为在产生自由能表面实际的系统中的实用工具.
关键词:  自由能,能级校正,加权直方图分析法,蒙特卡罗重采样
DOI:10.1063/1674-0068/cjcp2001001
分类号: