{"id":18708966,"url":"https://github.com/abelcarreras/gromorg","last_synced_at":"2025-09-15T21:03:56.361Z","repository":{"id":57436090,"uuid":"375767558","full_name":"abelcarreras/gromorg","owner":"abelcarreras","description":"A python GROMACS interface for MD simulations of organic molecular crystals","archived":false,"fork":false,"pushed_at":"2022-12-15T14:46:38.000Z","size":273,"stargazers_count":2,"open_issues_count":0,"forks_count":2,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-03-26T05:41:53.422Z","etag":null,"topics":["gromacs","molecular-dynamics","molecular-mechanics","python","simulation"],"latest_commit_sha":null,"homepage":"https://gromorg.readthedocs.io","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/abelcarreras.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2021-06-10T16:46:28.000Z","updated_at":"2023-01-03T18:30:29.000Z","dependencies_parsed_at":"2023-01-29T03:30:18.179Z","dependency_job_id":null,"html_url":"https://github.com/abelcarreras/gromorg","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/abelcarreras%2Fgromorg","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/abelcarreras%2Fgromorg/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/abelcarreras%2Fgromorg/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/abelcarreras%2Fgromorg/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/abelcarreras","download_url":"https://codeload.github.com/abelcarreras/gromorg/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248553823,"owners_count":21123526,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["gromacs","molecular-dynamics","molecular-mechanics","python","simulation"],"created_at":"2024-11-07T12:25:50.336Z","updated_at":"2025-09-15T21:03:51.283Z","avatar_url":"https://github.com/abelcarreras.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![Documentation Status](https://readthedocs.org/projects/gromorg/badge/?version=latest)](https://gromorg.readthedocs.io/en/latest/?badge=latest)\n[![PyPI version](https://badge.fury.io/py/gromorg.svg)](https://badge.fury.io/py/gromorg)\n\n\nGroMorG\n=======\n\nA python tool to automate the calculation of MD simulations of small organic molecules using gromacs.  \nOnline documentation is available at https://gromorg.readthedocs.io/\n\nFeatures\n--------\n- Link first principles \u0026 molecular mechanics calculations using PyQchem\n- Get parameters from SwissParam (https://www.swissparam.ch) automatically from molecular structure\n- Clean run without intermediate files\n- Add solvent molecules to the system\n- Extract structures from the trajectory (including surrounding solvent molecules)\n\nRequirements\n------------\n- PyQchem (https://github.com/abelcarreras/PyQchem)\n- Gromacs (gmxapi) (http://www.gromacs.org)\n- Openbabel v2.x (python API) (http://openbabel.org)\n- MDtraj (https://www.mdtraj.org)\n\nBasic example\n-------------\n```python\nfrom gromorg import GromOrg\nimport matplotlib.pyplot as plt\nfrom pyqchem.structure import Structure\n\n# Define moleule as PyQchem Structure\nstructure = Structure(coordinates=[[ 0.6695, 0.0000, 0.0000],\n                                   [-0.6695, 0.0000, 0.0000],\n                                   [ 1.2321, 0.9289, 0.0000],\n                                   [ 1.2321,-0.9289, 0.0000],\n                                   [-1.2321, 0.9289, 0.0000],\n                                   [-1.2321,-0.9289, 0.0000]],\n                      symbols=['C', 'C', 'H', 'H', 'H', 'H'])\n\n# Define Gromacs parameters\ngmx_params = {\n             'integrator': 'md-vv',     # Verlet integrator\n             'nsteps': 5000,            # 0.001 * 5000 = 50 ps\n             'dt': 0.001,               # time step, in ps\n             # Temperature coupling is on\n             'tcoupl': 'nose-hoover',    # Nose-Hoover thermostat\n             'tau_t': 0.3,               # time constant, in ps\n             'ref_t': 300,               # reference temperature, one for each group, in K\n             # Bond parameters\n             'gen_vel': 'yes',           # assign velocities from Maxwell distributio\n             'gen_temp': 300,            # temperature for Maxwell distribution\n             'gen_seed': -1,             # generate a random seed\n             }\n\n# Define simulation\ncalc = GromOrg(structure, \n               params=gmx_params,        # MDP parms \n               box=[10, 10, 10],         # a, b, c in angstrom\n               angles=[90, 90, 90],      # alpha, beta, gamma in degree\n               supercell=[3, 3, 3],\n               delete_scratch=True,      # delete temp files when finished\n               silent=False)             # print MD log info in screen\n\n# Run simulation and get trajectory (MDTraj) and energy\ntrajectory, energy = calc.run_md(whole=True) \n\n# plot energies\nplt.plot(energy['potential'], label='potential')\nplt.plot(energy['kinetic'], label='kinetic')\nplt.plot(energy['total'], label='total')\nplt.legend()\nplt.show()\n\n# Store trajectory\ntrajectory.save('trajectory.gro')\n```\n\nContact info\n------------\nAbel Carreras  \nabelcarreras83@gmail.com\n\nDonostia International Physics Center (DIPC)  \nDonostia-San Sebastian, Euskadi (Spain)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fabelcarreras%2Fgromorg","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fabelcarreras%2Fgromorg","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fabelcarreras%2Fgromorg/lists"}