Simulation files for "Interfacial water is separated from a hydrophobic silica surface by a gap of 1.2 nm"

This is the simulation data set for the manuscript: Arvelo DM, Comer J, Schmit J, Garcia R (2024) Interfacial water is separated from a hydrophobic silica surface by a gap of 1.2 nm. ACS Nano 18:18683–18692. https://doi.org/10.1021/acsnano.4c05689 This data set includes all files needed to run and analyze the simulations described in the this manuscript in the molecular dynamics software NAMD, as well as the output of the simulations. LAMMPS input files for the ReaxFF simulations are also included. The files are organized into directories corresponding to the figures of the main text and supporting information. They include molecular model structure files (NAMD psf or LAMMPS data), force field parameter files (in CHARMM format or ReaxFF format), initial atomic coordinates (pdb format), NAMD or LAMMPS configuration files, Colvars configuration files, NAMD or LAMMPS log files, and output including restart files (in binary NAMD format) and trajectories in dcd format (downsampled with a stride of 100 to 20 ns per frame). Analysis is controlled by shell scripts (Bash-compatible) that call VMD Tcl scripts or python scripts. These scripts and their output are also included. Version: 1.0 SIMULATION DATA=============== Figure5AC: Simulation of pentadecane on a 5 chains/nm^2 OTS layer. Figure5B_FigureS7: Calculation of force profile for an SiO2 tip asperity model using adaptive biasing force. Systems: octane with 5 chains/nm^2 OTS, octane with 4 chains/nm^2 OTS, decane with 5 chains/nm^2 OTS, water with 5 chains/nm^2 OTS FigureS6: Simulations showing the effect of octadecane on the structure of the OTS layer for 3 and 5 chains/nm^2 densities. FigureS8: Calculation of the adsorption free energy of tetracosane (C24) at the OTS–water interface using ABF. FigureS9: Python script for estimating the critical concentration to form an alkane layer at the OTS–water interface using the mean-field Ising model. FigureS10: ReaxFF simulation and modeling to create the silanol-terminated amorphous silica model of an AFM tip asperity. FigureS11: Molecular dynamics simulations showing spontaneous assembly of twelve or twenty-four tetracosane (C24) molecules at the interface between water and the alkyl groups of an OTS-conjugated silica surface. Conventions Used in These Files=============================== Structure Files----------------- bigSiO2-OTS-d5.psf (original NAMD (XPLOR?) format psf file including atom details (type, charge, mass), as well as definitions of bonds, angles, dihedrals, and impropers for each dipeptide.) - bigSiO2-OTS-d5.pdb (initial coordinates before minimization or equilibration)- repart_*.psf (same as the above psf files, but the masses of non-water hydrogen atoms have been repartitioned by VMD script repartitionMass.tcl)- freeTop*.pdb (same as the above pdb files, but atoms have been marked for restraints in NAMD. These files are generated by step1_prep.sh, with restraints applied to some silicon atoms in the solid SiO2 slab.) Force Field Parameters----------------------CHARMM format parameter files:- par_all36_cgenff_cgenff.prm (CHARMM36 CHARRM General Force Field with NBFIX terms for these same atoms)- toppar_water_ions_cgenff.str (CHARMM water and ions with NBFIX parameters needed for CGenFF and others commented out)- par_silica_Heinz_v2.prm (Parameters for SiO2 Based on Emami, ..., Heinz. Chem. Mater. 2014, 26, 2647−2658 https://doi.org/10.1021/cm500365c) Template NAMD Configuration Files---------------------------------These contain the most commonly used simulation parameters. They are called by the other NAMD configuration files (which are in the namd/ subdirectory):- template_min.namd (minimization)- template_eq.namd (NPT equilibration)- template_prod.namd (for the long production simulations)- template_abf.namd (applying adaptive biasing force) Minimization-------------- namd/min_*.0.namd Equilibration-------------- namd/eq_*.0.namd Production----------- namd/prod_*.[0-9].namd (The run number [0-9] is incremented when the simulation is continued) Free energy or Force Calculation--------------------------------- namd/abf0_*.[0-9].namd (The run number [0-9] is incremented when the simulation is continued)- namd/abf1_*.[0-9].namd (A replicate of the above)- namd/abf2_*.[0-9].namd (A replicate of the above) Scripts-------Files with the .sh extension can be found throughout. These usually provide the highest level control for submission of simulations and analysis. Look to these as a guide to what is happening.本数据集为以下学术论文的配套模拟数据： Arvelo DM, Comer J, Schmit J, Garcia R (2024) 界面水与疏水二氧化硅表面间距为1.2 nm的间隙。ACS Nano 18:18683–18692. https://doi.org/10.1021/acsnano.4c05689 本数据集包含利用分子动力学软件NAMD（Nanoscale Molecular Dynamics）运行、分析该论文所述模拟所需的全部文件，以及模拟输出结果；同时附带了ReaxFF反应力场（ReaxFF）模拟所用的LAMMPS输入文件。 所有文件按照正文中的图及辅助信息图对应的目录进行组织，涵盖以下类型文件： - 分子模型结构文件（NAMD PSF格式或LAMMPS数据格式） - 力场参数文件（CHARMM格式或ReaxFF格式） - 初始原子坐标文件（PDB格式） - NAMD或LAMMPS配置文件 - Colvars（集体变量模块）配置文件 - NAMD或LAMMPS日志文件 - 各类输出文件：包括二进制NAMD格式的重启文件，以及DCD格式的轨迹文件（已以步长100进行下采样，每帧对应20 ns的模拟时长）。 分析流程通过兼容Bash的Shell脚本控制，此类脚本会调用VMD（Visual Molecular Dynamics）Tcl脚本或Python脚本，相关脚本及其输出结果均已包含在数据集中。 版本：1.0 ====== 模拟数据 ====== - 图5AC：五癸烷在5条链/nm² 十八烷基三氯硅烷（Octadecyltrichlorosilane, OTS）单层上的模拟 - 图5B_辅助图S7：采用自适应偏置力（Adaptive Biasing Force, ABF）计算SiO₂针尖粗糙模型的力分布曲线，涉及体系包括：辛烷与5条链/nm² OTS体系、辛烷与4条链/nm² OTS体系、癸烷与5条链/nm² OTS体系、水与5条链/nm² OTS体系 - 辅助图S6：模拟十八烷对密度为3条链/nm²及5条链/nm²的OTS单层结构的影响 - 辅助图S8：采用自适应偏置力（ABF）计算二十四烷（C₂₄）在OTS-水界面的吸附自由能 - 辅助图S9：基于平均场伊辛模型，估算在OTS-水界面形成烷烃层所需临界浓度的Python脚本 - 辅助图S10：构建原子力显微镜（Atomic Force Microscope, AFM）针尖粗糙模型的硅羟基封端无定形二氧化硅的ReaxFF模拟与建模 - 辅助图S11：分子动力学模拟，展示十二或二十四烷烃（C₂₄）分子在水与OTS共轭二氧化硅表面烷基基团的界面处自发组装的过程 ====== 文件使用规范 ====== ### 结构文件 - bigSiO2-OTS-d5.psf：原始NAMD（XPLOR？格式）PSF文件，包含原子细节（类型、电荷、质量），以及每个二肽的键、角、二面角和improper二面角的定义 - bigSiO2-OTS-d5.pdb：最小化或平衡前的初始坐标文件 - repart_*.psf：与上述PSF文件内容一致，但非水氢原子的质量已通过VMD脚本repartitionMass.tcl重新分配 - freeTop*.pdb：与上述PDB文件内容一致，但已标记NAMD中的约束原子；此类文件由step1_prep.sh生成，对固体SiO₂块体中的部分硅原子施加了约束 ### 力场参数文件 - CHARMM格式参数文件： - par_all36_cgenff_cgenff.prm：CHARMM36通用力场（CGenFF），包含针对本研究所用原子的NBFIX项 - toppar_water_ions_cgenff.str：适用于CGenFF等的CHARMM水和离子参数文件，相关注释项已被移除 - par_silica_Heinz_v2.prm：基于Emami等人2014年发表的研究（Chem. Mater. 2014, 26, 2647−2658, https://doi.org/10.1021/cm500365c）的SiO₂力场参数 ### NAMD配置模板文件 此类文件包含最常用的模拟参数，由NAMD子目录下的其他NAMD配置文件调用： - template_min.namd：最小化模拟模板 - template_eq.namd：NPT（恒压恒温）平衡模拟模板 - template_prod.namd：长时程生产模拟模板 - template_abf.namd：应用自适应偏置力的模拟模板 ### 最小化流程 namd/min_*.0.namd ### 平衡流程 namd/eq_*.0.namd ### 生产模拟 namd/prod_*.[0-9].namd（当模拟续跑时，运行编号[0-9]会递增） ### 自由能或力计算 namd/abf0_*.[0-9].namd（模拟续跑时运行编号递增） namd/abf1_*.[0-9].namd：上述计算的重复实验组 namd/abf2_*.[0-9].namd：上述计算的重复实验组 ### 脚本文件 全目录中均包含扩展名为.sh的文件，此类文件通常提供最高层级的模拟提交与分析控制流程，可作为了解整体模拟与分析流程的参考依据。