Comparison of the efficiency of equilibrium and nonequilibrium molecular dynamic simulations of molecular solvation free energies

doi:10.3969/j.issn.1000-5641.2019.01.010

Abstract

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.

Key words: solvation free energies, side chain analogs of amino acids, equilibrium molecular dynamic simulations, nonequilibrium molecular dynamic simulations

CLC Number:

O469

LI Peng-fei, WANG Mei-ting, MEI Ye. Comparison of the efficiency of equilibrium and nonequilibrium molecular dynamic simulations of molecular solvation free energies[J]. Journal of East China Normal University(Natural Sc, 2019, 2019(1): 83-92.

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