# \#python **URL:** https://gromacs.bioexcel.eu/tag/python/53.md [Latest](https://gromacs.bioexcel.eu/latest.md) · [Categories](https://gromacs.bioexcel.eu/categories.md) · [Tags](https://gromacs.bioexcel.eu/tags.md) --- ## [\[TOOL\] GROMACS Trajectory Displayer — Web Dashboard for Trajectory Analysis & Visualization](https://gromacs.bioexcel.eu/t/tool-gromacs-trajectory-displayer-web-dashboard-for-trajectory-analysis-visualization/13633)
**Author:** [@AyushSingh009](https://gromacs.bioexcel.eu/u/AyushSingh009)\ **Replies:** 0\ **Last updated:** [July 30, 2026, 8:15am UTC](https://gromacs.bioexcel.eu/t/tool-gromacs-trajectory-displayer-web-dashboard-for-trajectory-analysis-visualization/13633 "2026-07-30T08:15:18Z")
Brief description of tools/files: GROMACS Trajectory Displayer (GROMACS Insight Platform) is an open-source, web-based interactive application built in Python. It provides a lightweight user interface to parse, process, … --- ## [Error in topology conversion from CGenFF](https://gromacs.bioexcel.eu/t/error-in-topology-conversion-from-cgenff/12304)
**Author:** [@Juan\_L](https://gromacs.bioexcel.eu/u/Juan_L)\ **Replies:** 0\ **Last updated:** [July 1, 2025, 7:27am UTC](https://gromacs.bioexcel.eu/t/error-in-topology-conversion-from-cgenff/12304 "2025-07-01T07:27:32Z")
GROMACS version: 2025 GROMACS modification: No Operating System: Ubuntu 24.04 Hello! I am a new user trying to learn Gromacs from Lemkul Labs’ GROMACS tutorial on Protein-Ligand. During conversion from CHARMM topolog… --- ## [Error in generating ligand topology using CGenFF python script](https://gromacs.bioexcel.eu/t/error-in-generating-ligand-topology-using-cgenff-python-script/5995)
**Author:** [@FreaX\_997](https://gromacs.bioexcel.eu/u/FreaX_997)\ **Replies:** 12\ **Last updated:** [January 8, 2025, 9:59am UTC](https://gromacs.bioexcel.eu/t/error-in-generating-ligand-topology-using-cgenff-python-script/5995 "2025-01-08T09:59:49Z")
GROMACS version: 2023 GROMACS modification: No Operating System: Ubuntu 22.10 Hello! This is an error I faced while following “Step Two: Prepare the Ligand Topology” of the Lemkul Labs’ GROMACS tutorial on Protein-Li… --- ## [Trouble with CGenFF and Ligand Topology in GROMACS](https://gromacs.bioexcel.eu/t/trouble-with-cgenff-and-ligand-topology-in-gromacs/10376)
**Author:** [@mostafagh98](https://gromacs.bioexcel.eu/u/mostafagh98)\ **Replies:** 0\ **Last updated:** [October 19, 2024, 8:03am UTC](https://gromacs.bioexcel.eu/t/trouble-with-cgenff-and-ligand-topology-in-gromacs/10376 "2024-10-19T08:03:59Z")
GROMACS version: 2023 GROMACS modification: No Python version: 3.12.2 Hi everyone, I come from a biology background, so my knowledge of programming is limited. I’m doing the protein-ligand tutorial from the mdtutorial… --- ## [Error in generating ligand topology using CGenFF and python 3.9](https://gromacs.bioexcel.eu/t/error-in-generating-ligand-topology-using-cgenff-and-python-3-9/8516)
**Author:** [@Ygya](https://gromacs.bioexcel.eu/u/Ygya)\ **Replies:** 1\ **Last updated:** [March 6, 2024, 7:23am UTC](https://gromacs.bioexcel.eu/t/error-in-generating-ligand-topology-using-cgenff-and-python-3-9/8516 "2024-03-06T07:23:31Z")
GROMACS version: 5.1.2 GROMACS modification: No Python version:3.9 After using this command python3 cgenff\_charmm2gmx\_py3\_nx2.py JZ4 jz4\_fixed.mol2 jz4.str charmm36-jul2022.ff ( I used this command to install network… --- ## [GROMACS hangs when run from python multiprocess](https://gromacs.bioexcel.eu/t/gromacs-hangs-when-run-from-python-multiprocess/6317)
**Author:** [@pipitoludovico](https://gromacs.bioexcel.eu/u/pipitoludovico)\ **Replies:** 22\ **Last updated:** [May 17, 2023, 10:28am UTC](https://gromacs.bioexcel.eu/t/gromacs-hangs-when-run-from-python-multiprocess/6317 "2023-05-17T10:28:58Z")
GROMACS version: 2022.4 GROMACS modification: No Here post your question Dear all, I have written a small python program that runs multiple simulations under Linux using multiprocessing to run a set of parallel simul… --- ## [New Python style requirements](https://gromacs.bioexcel.eu/t/new-python-style-requirements/5091)
**Author:** [@ericirrgang](https://gromacs.bioexcel.eu/u/ericirrgang)\ **Replies:** 0\ **Last updated:** [October 23, 2022, 1:12pm UTC](https://gromacs.bioexcel.eu/t/new-python-style-requirements/5091 "2022-10-23T13:12:44Z")
!3217 has just been merged, which adds a Python code formatting check to the first stage automated testing pipe line. (Brief notes have been added to Guidelines for code formatting - GROMACS 2023-dev-20221022-fd97a15 do… --- ## [Problem building gmxapi Python package](https://gromacs.bioexcel.eu/t/problem-building-gmxapi-python-package/4417)
**Author:** [@shivam1](https://gromacs.bioexcel.eu/u/shivam1)\ **Replies:** 5\ **Last updated:** [July 7, 2022, 2:05pm UTC](https://gromacs.bioexcel.eu/t/problem-building-gmxapi-python-package/4417 "2022-07-07T14:05:43Z")
@ericirrgang Hello everyone, I installed Gromacs with GMXAPI=ON (please see the command below) but when I try to import gmx in a python script (import gmxapi as gmx) it shows Module Error: No module name gmxapi cmak… --- ## [Python gmxapi.error](https://gromacs.bioexcel.eu/t/python-gmxapi-error/856)
**Author:** [@btam125](https://gromacs.bioexcel.eu/u/btam125)\ **Replies:** 8\ **Last updated:** [July 5, 2022, 9:44pm UTC](https://gromacs.bioexcel.eu/t/python-gmxapi-error/856 "2022-07-05T21:44:40Z")
GROMACS version:Version 2020 GROMACS modification: No Here post your question Dear all, I am trying to incorporate python in order to simplify my work, this is the code that I have written: import gmxapi as gmx tra… --- ## [Running gromacs with python](https://gromacs.bioexcel.eu/t/running-gromacs-with-python/851)
**Author:** [@btam125](https://gromacs.bioexcel.eu/u/btam125)\ **Replies:** 4\ **Last updated:** [June 3, 2021, 10:29am UTC](https://gromacs.bioexcel.eu/t/running-gromacs-with-python/851 "2021-06-03T10:29:39Z")
GROMACS version: 2020 GROMACS modification: No Here post your question Dear all, I am trying to run python by following this link: http://manual.gromacs.org/current/gmxapi/userguide/usage.html I have successfully a… --- ## [Bug in the python code?](https://gromacs.bioexcel.eu/t/bug-in-the-python-code/1108)
**Author:** [@btam125](https://gromacs.bioexcel.eu/u/btam125)\ **Replies:** 3\ **Last updated:** [November 19, 2020, 12:40am UTC](https://gromacs.bioexcel.eu/t/bug-in-the-python-code/1108 "2020-11-19T00:40:06Z")
GROMACS version:2020 GROMACS modification: No Here post your question Hi all, I have written a python code which work previously: pdb2gmx = gmx.commandline\_operation(‘gmx\_mpi’, arguments =\[‘pdb2gmx’\], input\_files={’…