Protex-A Python']Python utility for proton exchange in molecular dynamics simulations

被引：5

作者：

Joerg, Florian ^{[1
,2
]}

Wieder, Marcus ^{[3
]}

Schroeder, Christian ^{[1
]}

机构：

[1] Univ Vienna, Fac Chem, Dept Computat Biol Chem, Vienna, Austria

[2] Univ Vienna, Vienna Doctoral Sch Chem DoSChem, Vienna, Austria

[3] Univ Vienna, Fac Life Sci, Dept Pharmaceut Sci, Vienna, Austria

来源：

FRONTIERS IN CHEMISTRY | 2023年 / 11卷

基金：

奥地利科学基金会;

关键词：

molecular dynamics; ionic liquids; dynamic properties; proton exchange; conductivity; FREE-ENERGY SIMULATIONS; VALENCE-BOND MODEL; CONSTANT-PH; PHYSICOCHEMICAL PROPERTIES; FORCE-FIELD; POLARIZATION; TRANSPORT; TERMS;

D O I：

10.3389/fchem.2023.1140896

中图分类号：

O6 [化学];

学科分类号：

0703 ;

摘要：

Protex is an open-source program that enables proton exchanges of solvent molecules during molecular dynamics simulations. While conventional molecular dynamics simulations do not allow for bond breaking or formation, protex offers an easy-to-use interface to augment these simulations and define multiple proton sites for (de-)protonation using a single topology approach with two different lambda-states. Protex was successfully applied to a protic ionic liquid system, where each molecule is prone to (de-)protonation. Transport properties were calculated and compared to experimental values and simulations without proton exchange.

引用

页数：13

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