A codebase for MD simulation setup and results analysis.
Project description
mdgo
A code base for classical molecualr dynamics (MD) simulation setup and results analysis.
Requirements
mdgo requires numpy, pandas, matplotlib, scipy, tqdm, statsmodels, pymatgen, pubchempy, selenium, MDAnalysis (version 2.0.0-dev0 prefered) and their dependencies.
Source Code
If not available already, use the following steps.
-
Install git, if not already packaged with your system.
-
Download the mdgo source code using the command::
git clone https://github.com/htz1992213/mdgo.git
Installation
-
Navigate to mdgo root directory:
cd mdgo
-
Install the code, using the command:
pip install .
-
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
-
Navigate to mdgo root directory:
cd mdgo
-
Install the code in "editable" mode, using the command::
pip install -e .
-
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.
Features
- Retriving compound structure and information from PubChem
- Supported searching text:
- cid, name, smiles, inchi, inchikey or formula
- Supported output format:
- XML, ASNT/B, JSON, SDF, CSV, PNG, TXT
- Supported searching text:
- Write OPLS-AA forcefield file from LigParGen
- Supported input format:
- mol/pdb
- SMILES code
- Supported output format:
- LAMMPS(.lmp)
- GROMACS(.gro, .itp)
- Supported input format:
- Write OPLS-AA forcefield file from Maestro
- Supported input format:
- Supported output format:
- LAMMPS(.lmp)
- Others pending...
- Packmol wrapper
- Supported input format:
- xyz
- Others pending...
- Supported input format:
- Basic simulation properties
- Initial box dimension
- Equilibrium box dimension
- Salt concentration
- Conductivity analysis
- Green--Kubo conductivity
- Nernst--Einstein conductivity
- 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
- Diffusion analysis
- The mean square displacement of all species
- The mean square displacement of coordinated species and uncoordinated species, separately
- Self-diffusion coefficients
- Residence time analysis
- The residence time of all species
Project details
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