Metadata-Version: 2.1
Name: mdgo
Version: 0.2.4
Summary: A codebase for MD simulation setup and results analysis.
Home-page: https://github.com/HT-MD/mdgo
Author: mdgo development team
Author-email: tingzheng_hou@berkeley.edu
Maintainer: Tingzheng Hou
Maintainer-email: tingzheng_hou@berkeley.edu
License: MIT
Description: # ![MDGO](https://github.com/HT-MD/mdgo/blob/main/docs/logo_mdgo.svg)
        
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        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](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.
        
        ## 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
        
          [format that Maestro support]: https://www.schrodinger.com/kb/1278
        
Keywords: LAMMPS,Gromacs,Molecular dynamics,liquid,charge,materials,science,solvation,diffusion,transport,conductivity,force field
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Topic :: Scientific/Engineering :: Information Analysis
Classifier: Topic :: Scientific/Engineering :: Physics
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Requires-Python: >=3.7
Description-Content-Type: text/markdown
Provides-Extra: web
