Welcome to PyGromosTools

General

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

General Information

Specifications

• Python >=3.7:

• requires: numpy, scipy, pandas, rdkit

• optional: openforcefield for OpenForceField and Serenityff functions

SETUP

see INSTALL.md file for more informations

Copyright

Copyright (c) 2020, Benjamin Ries, Marc Lehner, Salome Rieder

Acknowledgements

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