Influence of the Treatment of Nonbonded Interactions on the Thermodynamic and Transport Properties of Pure Liquids Calculated Using the 2016H66 Force Field

被引:28
|
作者
Goncalves, Yan M. H. [1 ]
Senac, Caroline [2 ]
Fuchs, Patrick F. J. [3 ,4 ]
Hunenberger, Philippe H. [5 ]
Horta, Bruno A. C. [1 ]
机构
[1] Univ Fed Rio de Janeiro, Inst Quim, BR-21941909 Rio De Janeiro, Brazil
[2] Sorbonne Univ, CNRS, INSERM, LIB, F-75006 Paris, France
[3] Sorbonne Univ, Ecole Normale Super, Lab Biomol, PSL Univ,CNRS,LBM, F-75005 Paris, France
[4] Univ Paris Diderot, F-75013 Paris, France
[5] Swiss Fed Inst Technol, Lab Phys Chem, CH-8093 Zurich, Switzerland
关键词
MOLECULAR-DYNAMICS SIMULATIONS; PARTICLE-MESH EWALD; INTERMOLECULAR POTENTIAL FUNCTIONS; LONG-RANGE INTERACTIONS; FREE-ENERGIES; PARAMETER SET; ELECTROSTATIC INTERACTIONS; DIELECTRIC-PROPERTIES; COMPUTER-SIMULATIONS; BOUNDARY-CONDITIONS;
D O I
10.1021/acs.jctc.8b00425
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
The effect of different treatments of the nonbonded interactions in simulations employing the recently introduced GROMOS-compatible 2016H66 force field is evaluated based on calculations carried out with the GROMACS software. This is done considering four thermodynamic and transport properties (pure liquid density, vaporization enthalpy, surface-tension coefficient, and self-diffusion constant) of 58 organic liquids representative of the chemical groups alcohol, ether, aldehyde, ketone, carboxylic acid, ester, amine, amide, thiol, sulfide, disulfide, and aromatic compounds, also including water (SPC model). A dipalmitoylphosphati-dylcholine bilayer system is considered as well. The simulated properties are found to be very sensitive to the treatment of the long-range dispersion interactions, notably for the least polar systems. In general, the treatment of the long-range electrostatic or Lennard-Jones interactions using homogeneous correction terms or lattice-sum approaches yield similar results, with punctual discrepancies. The combination of a lattice-sum approach for the electrostatic interactions with a straight-cutoff truncation of the Lennard-Jones interactions at a distance of at least 1.2 nm is found to represent a good compromise setup within GROMACS for achieving compatibility with the reference results obtained using GROMOS as well as a comparable level of agreement with the experimental data. This study also reveals two potential issues with the GROMACS software, related to an incorrect calculation of the pressure when using LINCS in version 4.0.7 and an inadequate implementation of the twin-range scheme in version 5.1.2.
引用
收藏
页码:1806 / 1826
页数:21
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