# \#gromacs **URL:** https://help.galaxyproject.org/tag/gromacs/529.md [Latest](https://help.galaxyproject.org/latest.md) · [Categories](https://help.galaxyproject.org/categories.md) · [Tags](https://help.galaxyproject.org/tags.md) --- ## [GROMACS Solvation Step High Throughput Molecular Dynamics and AnalysisTutorial](https://help.galaxyproject.org/t/gromacs-solvation-step-high-throughput-molecular-dynamics-and-analysistutorial/16294)
**Author:** [@liz\_wright](https://help.galaxyproject.org/u/liz_wright)\ **Replies:** 3\ **Last updated:** [February 25, 2026, 10:45pm UTC](https://help.galaxyproject.org/t/gromacs-solvation-step-high-throughput-molecular-dynamics-and-analysistutorial/16294 "2026-02-25T22:45:59Z")
I am getting an error message when I run the GROMACS solvation step for the tutorial on High Throughput Molecular Dynamics and Analysis. The log file for this step indicates that the error is Fatal error: number of coo… --- ## [GROMACS simulation thread allocation](https://help.galaxyproject.org/t/gromacs-simulation-thread-allocation/17399)
**Author:** [@MGStejeda](https://help.galaxyproject.org/u/MGStejeda)\ **Replies:** 1\ **Last updated:** [February 2, 2026, 3:57pm UTC](https://help.galaxyproject.org/t/gromacs-simulation-thread-allocation/17399 "2026-02-02T15:57:12Z")
Hello Galaxy Team, I am encountering a recurring error with the GROMACS simulation tool in my workflow. My jobs are failing intermittently with the following fatal error: “The total number of threads requested (8) is n… --- ## [GROMACS Initial Setup Error](https://help.galaxyproject.org/t/gromacs-initial-setup-error/16520)
**Author:** [@i3l\_ezekielmeliala](https://help.galaxyproject.org/u/i3l_ezekielmeliala)\ **Replies:** 3\ **Last updated:** [December 15, 2025, 7:14pm UTC](https://help.galaxyproject.org/t/gromacs-initial-setup-error/16520 "2025-12-15T19:14:55Z")
Hello, I am currently trying out the “Hands on: High Throughput Molecular Dynamics and Analysis” tutorial with other data and ran into a problem with the ‘GROMACS Initial Setup” tool. Despite having no errors with the s… --- ## [GROMACS NVT & NPT energy equilibration not available anymore](https://help.galaxyproject.org/t/gromacs-nvt-npt-energy-equilibration-not-available-anymore/16429)
**Author:** [@Nicolas\_Caramello](https://help.galaxyproject.org/u/Nicolas_Caramello)\ **Replies:** 1\ **Last updated:** [October 27, 2025, 5:43pm UTC](https://help.galaxyproject.org/t/gromacs-nvt-npt-energy-equilibration-not-available-anymore/16429 "2025-10-27T17:43:10Z")
(topic deleted by author) --- ## [Forcefield.itp File not found during gromacs run despite uploading](https://help.galaxyproject.org/t/forcefield-itp-file-not-found-during-gromacs-run-despite-uploading/15178)
**Author:** [@swaroop25](https://help.galaxyproject.org/u/swaroop25)\ **Replies:** 1\ **Last updated:** [April 8, 2025, 5:51pm UTC](https://help.galaxyproject.org/t/forcefield-itp-file-not-found-during-gromacs-run-despite-uploading/15178 "2025-04-08T17:51:02Z")
I have uploaded all the charmm files and tried running the customised nvt step using Gromacs 2020.4 but I got the error that the forcefield.itp is not available. I have attached the screenshot for better understanding. … --- ## [PDB format versus PQR format](https://help.galaxyproject.org/t/pdb-format-versus-pqr-format/14041)
**Author:** [@doughfanb](https://help.galaxyproject.org/u/doughfanb)\ **Replies:** 2\ **Last updated:** [December 14, 2024, 10:12am UTC](https://help.galaxyproject.org/t/pdb-format-versus-pqr-format/14041 "2024-12-14T10:12:44Z")
Hi. I uploaded my protein in pdb but galaxy is identifying the format as pqr. What can I do about this? --- ## [GROMACS initial setup](https://help.galaxyproject.org/t/gromacs-initial-setup/13725)
**Author:** [@henrrik\_prendushi](https://help.galaxyproject.org/u/henrrik_prendushi)\ **Replies:** 4\ **Last updated:** [October 29, 2024, 11:17am UTC](https://help.galaxyproject.org/t/gromacs-initial-setup/13725 "2024-10-29T11:17:03Z")
Hi I’m in “GROMACS initial setup of topology and GRO structure file” I have specified the necessary parameters and uploaded my PDB file to the history. It is green. I try to run the app but it says “No pdb datasets av… --- ## [Troubleshooting Generate MD topologies for small molecules](https://help.galaxyproject.org/t/troubleshooting-generate-md-topologies-for-small-molecules/13780)
**Author:** [@henrrik\_prendushi](https://help.galaxyproject.org/u/henrrik_prendushi)\ **Replies:** 7\ **Last updated:** [November 7, 2024, 5:31pm UTC](https://help.galaxyproject.org/t/troubleshooting-generate-md-topologies-for-small-molecules/13780 "2024-11-07T17:31:02Z")
Dear Friends I’m studying “High Throughput Molecular Dynamics and Analysis,” and several times, using the recommended data, I have the results (in my history) in red (Error) for “Generate MD topologies for small molecul… --- ## [Error in GROMACS solvation and ading ions](https://help.galaxyproject.org/t/error-in-gromacs-solvation-and-ading-ions/13671)
**Author:** [@SALSABILA\_AQILAPUTRI](https://help.galaxyproject.org/u/SALSABILA_AQILAPUTRI)\ **Replies:** 1\ **Last updated:** [October 15, 2024, 6:47pm UTC](https://help.galaxyproject.org/t/error-in-gromacs-solvation-and-ading-ions/13671 "2024-10-15T18:47:35Z")
How to fix error output of gromacs solvation and adding ions?