Effect of Ions on the Aqueous-Phase Adsorption of Small Aromatic Organics on Silver

This repository contains sample calculations for our manuscript titled: " Effect of Ions on the Aqueous-Phase Adsorption of Small Aromatic Organics on Silver".

Repository Structure

1. ITP_files

This folder contains .itp files (molecular topology) for different organics used in the study.

2. Adsorption

The tar file consists of a sample calculation set-up for adsorption study performed in this work. It consists of four sub-folder namely analysis, MDP, PMF, System, and UMs.

• System folder contains following files:

  • sys#.gro files where # can be anything from 1 to 16. Each of these sys#.gro file consist of system structure with phenol at a distance away from the surface.
  • phenol.itp file consist of the molecular topology for phenol
  • topol.top file consists of main topology file for simulation. It includes various .itp files, includes atomtypes, nonbonded-parameters, and lists all molecules and their counts
  • index.ndx file consists of custom atom groups for analysis and restraints used in the simulation which makes it easy to reference a sub-group of atoms.
  • make_gro folder consists of various files used to create initial sys#.gro files.

• MDP folder contains different .mdp files (molecular dynamics parameters) to define simulation settings.

  • em.mdp is used for energy minimization step
  • nvt.mdp is used for equilibration with NVT ensemble
  • um.mdp is used for production run for each umbrella

• UMs folder consisting of different energy minimization, equilibration, and production data for each umbrella windows generated at the end of simulation.

• gather.sh file can be used to collect all .xvg and .tpr files into analysis folder which could be used for WHAM or force integration.

• PMF folder consists of .xvg files from each umbrella window and scripts for generating free energy profile.

3. Contact_angle_frames_and_script

The zip file consists of script used for contact angle measurement contact-angle-run.py and a folder frames_pure_water containing various frames for a sample contact angle run.

4. Solvation

The zip file consists of a sample calculation set-up for solvation study performed in this work. It consists of four sub-folder namely Equil, MDP, solMD, and System.

• System folder contains following files:

  • sys#.gro files where # can be anything from 1 to 16. Each of these sys#.gro file consist of system structure with phenol at a distance away from the surface.
  • phenol.itp file consist of the molecular topology for phenol
  • topol.top file consists of main topology file for simulation. It includes various .itp files, includes atomtypes, nonbonded-parameters, and lists all molecules and their counts
  • index.ndx file consists of custom atom groups for analysis and restraints used in the simulation which makes it easy to reference a sub-group of atoms.
  • make_gro folder consists of various files used to create initial sys#.gro files.

• MDP folder contains different .mdp files (molecular dynamics parameters) to define simulation settings.

  • em.mdp is used for energy minimization step
  • nvt.mdp is used for equilibration with NVT ensemble
  • npt.mdp is used for equilibration with NPT ensemble
  • md_solvation.mdp is used for production run for each lambda

• Equil folder consists initial system energy minimization and equilibration from run.

• solMD folder consists of output from the simulation consisting of:

  • Sub-folders named Lambda_#, where # is 0 to 29 with each # representing a value of $\lambda$ specified in md_solvation.mdp.
  • XVG folder consists of .xvg files obtained from Lambda_# folders.

Usage Instructions

Feel free to use any of the sample cases and scripts.

The QDyn set-up used in Gromacs is referenced from https://doi.org/10.1103/PhysRevLett.131.248001.