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This package is a python library with tools for the Molecular Simulation - Software Gromos. It allows you to easily set up, manage and analyze simulations in python.

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Welcome to PyGromosTools

CI pre-commit codecov Language grade: Python DOI Documentation

Description

The aim of the module is to bring GROMOS to the Python3 World! This repository should make it easier to work with GROMOS in Python and should enable the user to write cleaner, more reliable and adaptable code.

General informations about functions can be found in our wiki and usage example for many general functions and theire relations are shown in jupyter notebooks in the examples in the example folder.

Content

  • GROMOS wrappers

    • GromosXX wrapper: for simulation execution
    • GromosPP wrapper: for GROMOS++ program usage
  • File handling of all GROMOS file types for automated creation/modification/analysis :

    • coordinate files CNF:
    • read and analyse CNF files
    • generate CNF files from RDKit
    • generate CNF files from SDF
    cnf = Cnf(input_value="file_name")
    print(cnf.GENBOX)
    • topology files:
    • create topologies from a forcefield
    • GROMOS 2016H66 / 54A7
    • OpenForceField
    • SerenityForceField
    • modify topologies
    • add new atoms
    • modify force parameters
    top = Top(input_value="file_path")
    top.add_new_SOLUTEATOM(ATNM=42)
    print(top)
    • simulation parameter files IMD
    • a wide option of templates provided
    • modify IMD files to fit your simulation
    imd = Imd(input_value="file_path")
    imd.INITIALISE.TEMPI = 137
    print(imd)
    
    • trajectories (tre, trc, trg, ...)
    • analyse trajectories with Pandas data frames
    • standard analysis like RSMD, RDF, ... for trc
    • auto saving of results for later use as hdf5
    • ene_ana like tools for tre
    • easy to add costume analysis tools
    trc = Trc(input_value="file_path")
    print(trc.rmsd().mean())
    • replica exchange files: repdat.dat
    • classes for single blocks of each of these files.
  • Automation and file management system gromos_system

    • offers clean file management for simulations
    • offers a high level of automation
    • equiped with simulation queuing system
    • includes many force fields
    ff=forcefield_system(name="openforcefield")
    gsys = Gromos_System(work_folder="dir", in_smiles="C1CCCCC1", auto_convert=True, Forcefield=ff)
    print(gsys)
  • Simulation Submission and Execution :

    • Different Types of Simulation modules, like MD, SD or Emin.
    • Can be executed locally or on a cluster
    • easy to automatize and combine with analysis routines

    Run on a local machine:

    from pygromos.files.gromos_system import Gromos_System
    from pygromos.simulations.hpc_queuing.submission_systems.local import LOCAL as subSystem
    from pygromos.simulations.modules.preset_simulation_modules import emin
    
    # define file paths
    root_dir = "./example_files/SD_Simulation"
    root_in_dir = root_dir+"/SD_input"
    cnf_path = root_in_dir+"/6J29_unitedatom_optimised_geometry.cnf"
    top_path = root_in_dir + "/6J29.top"
    sys_name = "6J29"
    
    # Build gromos System
    grom_system = Gromos_System(in_cnf_path=cnf_path, in_top_path=top_path,
                                system_name=sys_name, work_folder=root_in_dir)
    # Run Emin
    emin_gromos_system, jobID = emin(in_gromos_system=grom_system, project_dir=root_dir,
                            step_name=step_name, submission_system=subSystem())

    Run on LSF-Cluster:

    from pygromos.files.gromos_system import Gromos_System
    from pygromos.simulations.hpc_queuing.submission_systems.lsf import LSF as subSystem
    from pygromos.simulations.modules.preset_simulation_modules import emin
    
    # define file paths
    root_dir = "./example_files/SD_Simulation"
    root_in_dir = root_dir+"/SD_input"
    cnf_path = root_in_dir+"/6J29_unitedatom_optimised_geometry.cnf"
    top_path = root_in_dir + "/6J29.top"
    sys_name = "6J29"
    
    # Build gromos System:
    grom_system = Gromos_System(in_cnf_path=cnf_path, in_top_path=top_path,
                            system_name=sys_name, work_folder=root_in_dir)
    
    # Run Emin
    sub_system = subSystem(nmpi=4) # allows parallelization
    emin_gromos_system, jobID = emin(in_gromos_system=grom_system, project_dir=root_dir,
                          step_name=step_name, submission_system=sub_system)
  • Other utilities:

    • Bash wrappers for GROMOS
    • Amino acid library

Quick Setup

Quick Start - move to the root folder of this repository:

  # build environment
  conda env create -f conda_env.yml
  conda develop -n pygromos ${PWD}

  # activate environment
  conda activate pygromos

Please make sure, that you have GROMOS (www.gromos.net) binaries around, if you want to use the MD-Package. We sadly can not provide the source code for this package, as it is currently not open-source.

If you find a bug or have an feature request, please raise an Issue on GitHub.

For more information, see INSTALL.md file for more informations.

Contributions

You want to contribute? Awesome! We are happy to support you in this process. For any contribution, please check out the CODE_OF_CONDUCT.md file and the style guide in styleguide.md. There will be a small code revision for code contributions, to verify that everything is in place.

Publications

Scientific Literature using PyGromosTools:

^ contributed equally

Acknowledgements

Many thanks to Robin Wolf for the logo design!

Copyright

Copyright (c) 2020, Benjamin Ries, Marc Lehner, Salome Rieder, Felix Pultar, Paul Katzberger, Candide Champion

Project based on the Computational Molecular Science Python Cookiecutter version 1.3.

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This package is a python library with tools for the Molecular Simulation - Software Gromos. It allows you to easily set up, manage and analyze simulations in python.

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