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

LI Peng-fei; WANG Mei-ting; MEI Ye

doi:10.3969/j.issn.1000-5641.2019.01.010

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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 Sciences), 2019, (1): 83-92. doi: 10.3969/j.issn.1000-5641.2019.01.010

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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 Sciences), 2019, (1): 83-92. doi: 10.3969/j.issn.1000-5641.2019.01.010

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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

State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China

Received Date: 2017-09-20
Publish Date: 2019-01-25

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.

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References

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