Coexistence and interfacial properties of triangle-well fluids

Coexistence and interfacial properties of triangle-well fluids are determined by combining the slab technique and the replica exchange algorithm for different interaction ranges (λ = 1.5, 1.75, 2.0, 2.5, and 3). This is implemented using both Monte Carlo and molecular dynamics methods. We make use of a recently proposed substitution of the hard-core repulsion by a linear function with a large negative slope. This makes possible to gain access through the virial route to thermodynamical properties and to employ widely spread packages such as Gromacs. Coexistence curves of these systems were calculated with both implementations and compared to those previously reported in the literature. A good agreement was found among them. Surface tension data obtained from Monte Carlo and molecular dynamics techniques also show a good agreement.     

Gro2mat: A package to efficiently read gromacs output in MATLAB

Molecular dynamics (MD) simulations are a state‐of‐the‐art computational method used to investigate molecular interactions at atomic scale. Interaction processes out of experimental reach can be monitored using MD software, such as Gromacs. Here, we present the gro2mat package that allows fast and easy access to Gromacs output files from Matlab. Gro2mat enables direct parsing of the most common Gromacs output formats including the binary xtc‐format. No openly available Matlab parser currently exists for this format. The xtc reader is orders of magnitudes faster than other available pdb/ascii workarounds. Gro2mat is especially useful for scientists with an interest in quick prototyping of new mathematical and statistical approaches for Gromacs trajectory analyses. © 2014 Wiley Periodicals, Inc.     

StreaMD: Advanced analysis of molecular dynamics using R

Gromacs is one of the most popular molecular simulation suites currently available. In this contribution we present streaMD , the first interface between Gromacs trajectory files and the statistical language R . The amount of data created due to ever increasing computational power renders fast and efficient analysis of trajectories into a challenge. Especially as standard approaches such as root‐mean square fluctuations and the like provide only limited physical insight. In our streaMD package integration of the Gromacs I/O libraries with advanced, graph‐based analysis methods as the java library Stream leads to both: improved speed and analysis depth. We benchmark our results and highlight the applicability of the package by an interesting problem in RNA design, namely the interaction of tetracycline with an aptamer. © 2018 Wiley Periodicals, Inc.     

基于分子动力学模拟的表面活性剂力场界面的构建及分析

以计算机模拟真实环境,根据分子动力学模拟原理以及相关应用,提出了使用分子优化软件,将分割后的分子片段在ATB网站上进行最终优化及拓扑文件的整合,并对抗盐性进行了试验验证,用在构建的界面中研究表面活性剂的活动轨迹以及离子对于此类表面活性剂的影响。在模拟过程中加入同一含量的Mg2+、Ca2+,考察这两种新型甜菜碱型两性离子表面活性剂在油水界面的密度分布及活动行为,从而研究表面活性剂结构和抗盐性之间的关系。研究结果表明,钙离子对NONA-CH3型甜菜碱界面行为的影响更为显著,它的抗盐性顺序为Na+Mg2+Ca2+;在相同外界条件下,NONA-CH2CH3的抗盐性能更优异。