rashatwi / mdgo

A codebase for classical molecular dynamics (MD) simulation setup and results analysis.

An all-in-one code base for the classical molecualr dynamics (MD) simulation setup and results analysis.

1. Installation

1.1 Installing from PyPI

To install the latest release version of mdgo:

pip install mdgo

1.2 Installing from source code

Mdgo requires numpy, pandas, matplotlib, scipy, tqdm, statsmodels, pymatgen>=2022.0.9, pubchempy, selenium, MDAnalysis (version 2.0.0-dev0 prefered) and their dependencies.

Getting Source Code

If not available already, use the following steps.

1. Install git, if not already packaged with your system.

2. Download the mdgo source code using the command:

   git clone https://github.com/htz1992213/mdgo.git

Installation

1. Navigate to mdgo root directory:

   cd mdgo

2. Install the code, using the command:

   pip install .

3. The latest version MDAnalysis==2.0.0.dev0 is recommended, you may download the source code of the latest MDAnalysis from github and install using pip to replace an existing version.

Installation in development mode

1. Navigate to mdgo root directory:

   cd mdgo

2. Install the code in "editable" mode, using the command::

   pip install -e .

3. The latest version MDAnalysis==2.0.0.dev0 is recommended, you may download the source code of the latest MDAnalysis from github and install using pip to replace an existing version.

2. Features

1. Retrieving compound structure and information from PubChem
   • Supported searching text:
     • cid, name, smiles, inchi, inchikey or formula
   • Supported output format:
     • smiles code, PDB, XML, ASNT/B, JSON, SDF, CSV, PNG, TXT
2. Retrieving water and ion models
   • Supported water models:
     • SCP, SPC/E, TIP3P_EW, TIP4P_EW, TIP4P_2005
   • Supported ion models:
     • alkali, ammonium, and halide monovalent ions by Jensen and Jorgensen
     • alkali and halide monovalent ions by Joung and Cheatham
     • alkali and alkaline-earth metal cations by Åqvist
3. Write OPLS-AA forcefield file from LigParGen
   • Supported input format:
     • mol/pdb
     • SMILES code
   • Supported output format:
     • LAMMPS(.lmp)
     • GROMACS(.gro, .itp)
4. Write OPLS-AA forcefield file from Maestro
   • Supported input format:
     • Any format that Maestro support
   • Supported output format:
     • LAMMPS(.lmp)
     • Others pending...
5. Packmol wrapper
   • Supported input format:
     • xyz
     • Others pending...
6. Basic simulation properties
   • Initial box dimension
   • Equilibrium box dimension
   • Salt concentration
7. Conductivity analysis
   • Green--Kubo conductivity
   • Nernst--Einstein conductivity
8. Coordination analysis
   • The distribution of the coordination number of single species
   • The integral of radial distribution function (The average coordination numbers of multiple species)
   • Solvation structure write out
   • Population of solvent separated ion pairs (SSIP), contact ion pairs (CIP), and aggregates (AGG)
   • The trajectory (distance) of cation and coordinating species as a function of time
   • The hopping frequency of cation between binding sites
   • The distribution heat map of cation around binding sites
   • The averaged nearest neighbor distance of a species
9. Diffusion analysis
   • The mean square displacement of all species
   • The mean square displacement of coordinated species and uncoordinated species, separately
   • Self-diffusion coefficients
10. Residence time analysis
    • The residence time of all species

3. Citation

When using MDAnalysis in published work, please cite the following paper:

• Hou, T.; Fong, K. D.; Wang, J.; Persson, K. A. The solvation structure, transport properties and reduction behavior of carbonate-based electrolytes of lithium-ion batteries. Chem. Sci. 2021, 12, 14740-14751. [doi]