Metadata-Version: 2.1
Name: mdgo
Version: 0.1.0
Summary: A codebase for MD simulation setup and results analysis.
Home-page: https://github.com/htz1992213/mdgo
Author: mdgo development team
Author-email: tingzheng_hou@berkeley.edu
Maintainer: Tingzheng Hou
Maintainer-email: tingzheng_hou@berkeley.edu
License: MIT
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.
        
        1. Install [git](http://git-scm.com), 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.
        
        Features
        ------------
        
        
        1.  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
        2.  Write OPLS-AA forcefield file from LigParGen
            -   Supported input format:
                -   mol/pdb
                -   SMILES code
            -   Supported output format:
                -   LAMMPS(.lmp)
                -   GROMACS(.gro, .itp)
        3.  Write OPLS-AA forcefield file from Maestro
            -   Supported input format:
                -   Any [format that Maestro support]
            -   Supported output format:
                -   LAMMPS(.lmp)
                -   Others pending\...
        4.  Packmol wrapper
            -   Supported input format:
                -   xyz
                -   Others pending\...
        5.  Basic simulation properties
            -   Initial box dimension
            -   Equilibrium box dimension
            -   Salt concentration
        6.  Conductivity analysis
            -   Green--Kubo conductivity
            -   Nernst--Einstein conductivity
        7.  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
        8.  Diffusion analysis
            -   The mean square displacement of all species
            -   The mean square displacement of coordinated species and
                uncoordinated species, separately
            -   Self-diffusion coefficients
        9.  Residence time analysis
            -   The residence time of all species
        
          [format that Maestro support]: https://www.schrodinger.com/kb/1278
        
Platform: UNKNOWN
Requires-Python: >=3.6
Description-Content-Type: text/markdown
Provides-Extra: web
