FREE-ENERGY SIMULATIONS OF METHANE SOLVATION - A STUDY OF INTEGRAND CONVERGENCE PROPERTIES USING THERMODYNAMIC INTEGRATION

被引:16
|
作者
FLEISCHMAN, SH [1 ]
ZICHI, DA [1 ]
机构
[1] AGOURON PHARMACEUT, SAN DIEGO, CA 92037 USA
关键词
D O I
10.1051/jcp/1991882617
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
This report presents the results of free energy simulations using thermodynamic integration (TI) to calculate the absolute free energy of solvation of methane. The dependence of the integrand on the form of the scaling of the Hamiltonian and the exten of the "growth" of the methane was studied. When the methane-water potential is scaled by between 0.002 and 0.15, the integrand became very noisy and the individual values had high statistical uncertainties. This region was responsible for the major contribution to the total integral. A value for the Helmholtz free energy of solvation of 1.23 kcal/mol was obtained, in comparison to the experimental value of 2.005 kcal/mol. It is evident that the calculation has not as yet converged.
引用
收藏
页码:2617 / 2622
页数:6
相关论文
共 50 条
  • [41] Calculation of the intrinsic solvation free energy profile of methane across a liquid/liquid interface in computer simulations
    Darvas, Maria
    Jorge, Miguel
    Cordeiro, M. Natalia D. S.
    Jedlovszky, Pal
    JOURNAL OF MOLECULAR LIQUIDS, 2014, 189 : 39 - 43
  • [42] EXAMINING ION CHANNEL PROPERTIES USING FREE-ENERGY METHODS
    Domene, Carmen
    Furini, Simone
    METHODS IN ENZYMOLOGY, VOL 466: BIOTHERMODYNAMICS, PT B, 2009, 466 : 155 - +
  • [43] Structural and Thermodynamic Investigations on the Aggregation and Folding of Acylphosphatase by Molecular Dynamics Simulations and Solvation Free Energy Analysis
    Chong, Song-Ho
    Lee, Chewook
    Kang, Guipeun
    Park, Mirae
    Ham, Sihyun
    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2011, 133 (18) : 7075 - 7083
  • [45] Efficiency of Alchemical Free Energy Simulations. II. Improvements for Thermodynamic Integration
    Bruckner, Stefan
    Boresch, Stefan
    JOURNAL OF COMPUTATIONAL CHEMISTRY, 2011, 32 (07) : 1320 - 1333
  • [46] CALCULATIONS OF RELATIVE FREE-ENERGY SURFACES IN CONFIGURATION SPACE USING AN INTEGRATION METHOD
    CUN, XW
    HAI, YL
    YUN, YS
    FU, HH
    CHEMICAL PHYSICS LETTERS, 1991, 179 (5-6) : 475 - 478
  • [47] Alchemical Free-Energy Calculations by Multiple-Replica λ-Dynamics: The Conveyor Belt Thermodynamic Integration Scheme
    Hahn, David F.
    Hunenberger, Philippe H.
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2019, 15 (04) : 2392 - 2419
  • [48] QM/MM free-energy perturbation compared to thermodynamic integration and umbrella sampling:: Application to an enzymatic reaction
    Kästner, J
    Senn, HM
    Thiel, S
    Otte, N
    Thiel, W
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2006, 2 (02) : 452 - 461
  • [49] Ion solvation free energy calculations based on first-principles molecular dynamics thermodynamic integration
    Lin, Chao
    He, Xiaojun
    Xi, Cong
    Zhang, Qianfan
    Wang, Lin-Wang
    JOURNAL OF CHEMICAL PHYSICS, 2024, 160 (18):
  • [50] Improving relative solvation and binding free energy calculations by augmenting Thermodynamic Integration with Hamiltonian Replica Exchange
    Khavrutskii, Ilja
    Wallqvist, Anders
    ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2011, 241