Emergence of the Robeson bound in non-equilibrium molecular dynamics simulations

Dual Control Volume Molecular Dyanmics (DCVMD)

OverView

This repository contains all the necessary data and instructions to reproduce the results published in Yuan et al., "Emergence of the Robeson bound in non-equilibrium molecular dynamics simulations". It is structured to facilitate running simulations, performing analyses, and interpreting results effectively.

Content

The repository is organized into the following key directories:

**`data/`**This folder includes all data files required for simulations and analyses. Key contents are:

- **GROMACS Files**: MDP files for running simulations such as energy minimization, NPT, and NVT simulations.- **Poreblazer Files**: Includes necessary files to perform Poreblazer analyses. The folder contains three essential files (defaults.dat,  DREIDING.atoms,  input.dat). Edit them accordingly to perform the calculations you want. - **Polymer Files**: Contains data for eight different membranes, including:  - Forcefield files (`ff.itp`)  - Position files (`out.gro`, `out.xyz` (relaxed structure for Poreblazer calculation) )  - Poreblazer input file (`input.dat`)  - Poreblazer results, such as:    - `probe_occupiable_volume.xyz`    - `summary.dat`    - `Total_psd.txt`

**`DCVMD/`**This folder includes a test case for the DCVMD method. Detailed instructions are provided to perform the test case on PIM-1. Simulations for other membranes can also be conducted using the data files available in the `data/` folder.

Usage Instructions

1. For the PIM-1 test case, use the files in the `DCVMD/` folder as a starting point. The instructions there will guide you for an example DCVMD simulation. 2. For custom membrane simulations, refer to the data provided in the `data/Polymer/` folder. Replace the membrane geometry and forcefield files as necessary.