Example Scripts for Two Ions in a Dipolar Solvent

Created by Chris Balzer. Distributed under the MIT Licence. Please cite our paper if you find this useful.

Overview

This repository contains the necessary input files to calculate one window of a potential of mean force (PMF) for two ions in a Stockmayer fluid based on the paper by Varner, Balzer, and Wang. Inputs are provided for symmetric ions (as explored in the paper) and for asymmetric ions (i.e. NaCl).

Contents

• input/: Input files
• output-asymmetric/: Output files for asymmetric ions
• output-symmetric/: Output files for asymmetric ions

Asymmetric System Description

1000 water molecules (0.03344 #/ $A^3$) at 300K with dipole moment 1.85 Debyes. Anion and cation are modeled after chlorine and sodium, respectively. The diameters (LJ $\sigma$) for each are 3.0 $A^3$, 3.62 $A^3$, 1.96 $A^3$ for water, Cl-, and Na+, respectively. The LJ unit of mass is 18.01528 g/mol. The LJ unit of length is 3.0 $A^3$. Water and NaCl parameters from Shock et al.

Symmetric System Description

1000 water molecules (0.03344 #/ $A^3$) at 300K with dipole moment 1.85 Debyes. Anion and cation are monovalent and symmetric in size. The diameters (LJ $\sigma$) for all components are 3.0 $A^3$. The LJ unit of mass is 18.01528 g/mol. The LJ unit of length is 3.0 $A^3$.

Note that this system size may be too small to accurately get long range electrostatics. Only for demonstration/testing.

Input Description

For each example, the distance betweem the two ions is constrained between 2.25 and 7.5 $A^3$ (0.75-2.5 $\sigma$). The LAMMPS files provided go through energy minimization, initialization, equilibration, and production. Dump and thermo outputs are less frequent for space saving in the example. - lammps.*.in - LAMMPS input file - system.data - Initial system configuration - input.colvars - Adaptive Biasing Force (ABF) input files to use the COLVARS package

Running the Example

To run the example, LAMMPS must be compiled. The examples have been verified to work on LAMMPS version as of 27 Jun 2024. Instructions to build LAMMPS can be found here. The packages required for this project are the DIPOLE, COLVARS, KSPACE, EXTRA-COMMANDS and MISC. For speed reasons, it may be advantageous to enable the GPU package. If using the GPU package, one can run the example using

lmp_gpu -sf gpu -pk gpu 1 -in lammps.*.in

Output Description

The output files are ... - log.lammps - LAMMPS log file - dump.dipoleInit,dump.dipoleEquil,dump.dipoleProd - Coordinates and dipole moment during initialization, equilibration, and production - equil.pmf, prod.pmf - The PMF calcualted from ABF - thermo.equil, thermo.prod - Energy output and instantaneous value of the ion separation