Comparison of the efficiency of equilibrium and nonequilibrium molecular dynamic simulations of molecular solvation free energies
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摘要: 着眼于13个中性氨基酸侧链类似物在水中的溶剂化自由能的计算，来比较两种计算自由能的平衡态动力学模拟和非平衡态动力学模拟方法在高性能计算机上的表现.研究发现，利用非平衡态动力学模拟来计算自由能除了在准确度上和平衡态动力学模拟的计算一致之外，在计算效率和实际所需时间上，非平衡方法计算效率更高，实际所需时间更少.Abstract: In this study, we used calculations to determine the solvation free energies of 13 side chain analogs of neutral amino acids in water to compare the performance of equilibrium and nonequilibrium molecular dynamic simulations on high-performance computers. We found that nonequilibrium molecular dynamic simulations have the same accuracy as equilibrium molecular dynamic simulations in calculations for solvation free energies. From the perspective of efficiency and computational cost, the nonequilibrium method is more efficient and requires less computational time.
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图 3 平衡态动力学方法计算的收敛性
Fig. 3 The convergence of hydration free energy calculated by the equilibrium dynamic method
图 4 非平衡态动力学方法计算的收敛性
Fig. 4 The convergence of hydration free energy calculated by the nonequilibrium dynamic method
表 1 氨基酸侧链类似物的简称
Tab. 1 Simplified names for side chain analogs of amino acids
氨基酸侧链类似物名称 对应氨基酸的简称 acetamide Asn methanethiol Cys propionamide Gln methanol Ser ethanol Thr n-butane Ile iso-butane Leu methylthioethane Met toluene Phe skatole Trp 4-methylphenol Tyr propane Val methane Ala 
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表 2 氨基酸侧链类似物在水中的溶剂化自由能
Tab. 2 Hydration free energy of side chain analogs of amino acids
kcal/mol 分子简称 平衡(MBAR) 非平衡(BAR) 实验值$^{a}$ Ala 2.41$\pm$0.02 2.33$\pm$0.06 1.94 Asn -9.58$\pm$0.04 -9.80$\pm$0.12 -9.68 Ile 2.51$\pm$0.03 2.50$\pm$0.12 2.15 Leu 2.30$\pm$0.03 2.19$\pm$0.11 2.28 Phe -0.69$\pm$0.04 -0.59$\pm$0.14 -0.76 Ser -4.71$\pm$0.03 -4.34$\pm$0.09 -5.06 Trp -5.45$\pm$0.04 -5.99$\pm$0.21 -5.88 Val 2.29$\pm$0.03 2.42$\pm$0.10 1.99 Cys -0.31$\pm$0.02 -0.59$\pm$0.08 -1.24 Gln -8.52$\pm$0.04 -8.53$\pm$0.14 -9.38 Met 0.48$\pm$0.03 0.61$\pm$0.12 -1.48 Thr -4.20$\pm$0.03 -3.93$\pm$0.09 -4.88 Tyr -4.68$\pm$0.04 -4.52$\pm$0.18 -6.11 RMSD 0.82 0.88 MSE 0.61 0.61
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