PyGromosTools

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.

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.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.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

GitHub

https://github.com/rinikerlab/PyGromosTools