DOI: 10.5281/zenodo.14855068
title: Simulation files for "Interfacial water is separated from a hydrophobic silica surface by a gap of 1.2 nm"

description: 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.