# \#gromacs **URL:** https://ask.bioexcel.eu/tag/gromacs/1.md [Latest](https://ask.bioexcel.eu/latest.md) · [Categories](https://ask.bioexcel.eu/categories.md) · [Tags](https://ask.bioexcel.eu/tags.md) --- ## [Using \`martinize2\` to get GōMartini coarse-grained protein parameters (Martini 3)](https://ask.bioexcel.eu/t/using-martinize2-to-get-gomartini-coarse-grained-protein-parameters-martini-3/6040)
**Author:** [@dheeraj.prakaash](https://ask.bioexcel.eu/u/dheeraj.prakaash)\ **Replies:** 0\ **Last updated:** [March 18, 2026, 3:08am UTC](https://ask.bioexcel.eu/t/using-martinize2-to-get-gomartini-coarse-grained-protein-parameters-martini-3/6040 "2026-03-18T03:08:58Z")
Hi all, After using martinize2 to successfully obtain Martini 3 coarse-grained (CG) protein structures a couple of years ago, I have recently been attempting the same, this time aiming to obtain GōMartini parameters rat… --- ## [NVT vs NPT for Non-Equilibrium Switching in pmx/GROMACS](https://ask.bioexcel.eu/t/nvt-vs-npt-for-non-equilibrium-switching-in-pmx-gromacs/5980)
**Author:** [@EidRashed](https://ask.bioexcel.eu/u/EidRashed)\ **Replies:** 1\ **Last updated:** [January 26, 2026, 11:19am UTC](https://ask.bioexcel.eu/t/nvt-vs-npt-for-non-equilibrium-switching-in-pmx-gromacs/5980 "2026-01-26T11:19:35Z")
I’m using pmx + GROMACS to run non-equilibrium alchemical free energy calculations for large protein–protein interactions (e.g., ~150 k atoms, like Fc–FcRn). My workflow is essentially: Equilibrate both end states (st… --- ## [Using PMX for ΔΔG on a glycosylated Fc (P238D back-mutation; PDB 3WJJ): viable workflows?](https://ask.bioexcel.eu/t/using-pmx-for-g-on-a-glycosylated-fc-p238d-back-mutation-pdb-3wjj-viable-workflows/5933)
**Author:** [@EidRashed](https://ask.bioexcel.eu/u/EidRashed)\ **Replies:** 5\ **Last updated:** [November 20, 2025, 3:29pm UTC](https://ask.bioexcel.eu/t/using-pmx-for-g-on-a-glycosylated-fc-p238d-back-mutation-pdb-3wjj-viable-workflows/5933 "2025-11-20T15:29:18Z")
Hi all, I’d like to use PMX to compute ΔΔG of binding for an Fc that is N-glycosylated (structure based on PDB: 3WJJ) by reversing the mutation P238D. I know PMX supports Amber and CHARMM family protein force fields out… --- ## [Absolute binding Free energy with NE-MD: Single-step complex leg & Boresch restraint tips](https://ask.bioexcel.eu/t/absolute-binding-free-energy-with-ne-md-single-step-complex-leg-boresch-restraint-tips/5840)
**Author:** [@ehsan](https://ask.bioexcel.eu/u/ehsan)\ **Replies:** 1\ **Last updated:** [August 4, 2025, 8:58am UTC](https://ask.bioexcel.eu/t/absolute-binding-free-energy-with-ne-md-single-step-complex-leg-boresch-restraint-tips/5840 "2025-08-04T08:58:51Z")
Hello PMX developers and users, I’m setting up an absolute binding free energy (ABFE) calculation using non-equilibrium MD with PMX/GROMACS, following the thermodynamic cycle (see attached image). Complex Leg (D → F) … --- ## [Protein-protein docking parameters](https://ask.bioexcel.eu/t/protein-protein-docking-parameters/5776)
**Author:** [@Negin](https://ask.bioexcel.eu/u/Negin)\ **Replies:** 2\ **Last updated:** [July 1, 2025, 9:48am UTC](https://ask.bioexcel.eu/t/protein-protein-docking-parameters/5776 "2025-07-01T09:48:29Z")
Hello I would like to perform protein-protein docking, and I do not have any experimental data showing how they are interacting and what is the binding interface of them. But, I used PesTo webserver and other online too… --- ## [(@marco.giulini) BioexcelWebinar#85: Modeling antibodies in the post-Alphafold era: Where are we now?](https://ask.bioexcel.eu/t/marco-giulini-bioexcelwebinar-85-modeling-antibodies-in-the-post-alphafold-era-where-are-we-now/5582)
**Author:** [@Alexandro926178](https://ask.bioexcel.eu/u/Alexandro926178)\ **Replies:** 17\ **Last updated:** [May 13, 2025, 4:51pm UTC](https://ask.bioexcel.eu/t/marco-giulini-bioexcelwebinar-85-modeling-antibodies-in-the-post-alphafold-era-where-are-we-now/5582 "2025-05-13T16:51:30Z")
Dear Marco Giulini, First of all, congratulations on your excellent participation! I am working with computational methods to elucidate the allergic mechanism triggered by polyethylene glycol used in the formulation of t… --- ## [Using biobb\_gromacs image on runpod](https://ask.bioexcel.eu/t/using-biobb-gromacs-image-on-runpod/5541)
**Author:** [@pducrot](https://ask.bioexcel.eu/u/pducrot)\ **Replies:** 2\ **Last updated:** [March 26, 2025, 4:48pm UTC](https://ask.bioexcel.eu/t/using-biobb-gromacs-image-on-runpod/5541 "2025-03-26T16:48:43Z")
Hi, I’m trying to run a Gromacs simulation using the biobb\_gromacs docker image running on runpod. It doesn’t seem to be using the GPU regardless the gmx mdrun options I set. In runpod I selected a RTX A4000 GPU pod. Do… --- ## [GROMACS Domain Decomposition Errors in Protein-Membrane Simulation with Martini](https://ask.bioexcel.eu/t/gromacs-domain-decomposition-errors-in-protein-membrane-simulation-with-martini/5452)
**Author:** [@mpapadourakis](https://ask.bioexcel.eu/u/mpapadourakis)\ **Replies:** 0\ **Last updated:** [March 5, 2025, 10:13am UTC](https://ask.bioexcel.eu/t/gromacs-domain-decomposition-errors-in-protein-membrane-simulation-with-martini/5452 "2025-03-05T10:13:48Z")
Hi all, I am attempting to simulate a protein-membrane system (60x60x25) using GROMACS 2024.4 with the Martini3 force field in the NPT ensemble. However, I am encountering domain decomposition errors immediately after m… --- ## [Pmx analyse says "no good dgdl files provided"](https://ask.bioexcel.eu/t/pmx-analyse-says-no-good-dgdl-files-provided/5394)
**Author:** [@mukherjee175](https://ask.bioexcel.eu/u/mukherjee175)\ **Replies:** 2\ **Last updated:** [January 13, 2025, 3:58pm UTC](https://ask.bioexcel.eu/t/pmx-analyse-says-no-good-dgdl-files-provided/5394 "2025-01-13T15:58:27Z")
I am working with a protein-peptide complex. I aim to do mutations on the peptide. I was performing mutation free energy calculations using the Fast growth method following the tutorial of the Trp cage. When I use pmx an… --- ## [Protein and cell membrane docking](https://ask.bioexcel.eu/t/protein-and-cell-membrane-docking/5379)
**Author:** [@xander](https://ask.bioexcel.eu/u/xander)\ **Replies:** 2\ **Last updated:** [December 26, 2024, 10:38am UTC](https://ask.bioexcel.eu/t/protein-and-cell-membrane-docking/5379 "2024-12-26T10:38:26Z")
I have anti-microbial peptide structure, and then i obtained a fungal membrane structure for a particular database, i want to perform docking between the anti-microbial peptide, as a ligand, and then the membrane as a re… --- ## [PMX AssertionError, Atom type OH not been defined in the force field, Atom DHD1 was not found](https://ask.bioexcel.eu/t/pmx-assertionerror-atom-type-oh-not-been-defined-in-the-force-field-atom-dhd1-was-not-found/5332)
**Author:** [@genetics](https://ask.bioexcel.eu/u/genetics)\ **Replies:** 3\ **Last updated:** [November 13, 2024, 8:57am UTC](https://ask.bioexcel.eu/t/pmx-assertionerror-atom-type-oh-not-been-defined-in-the-force-field-atom-dhd1-was-not-found/5332 "2024-11-13T08:57:57Z")
I am using developmental version of PMX. Python 3.11.0. Gromacs version 2024.4. I am trying to mutate 276 residue from R2W. My WT.pdb file has total 320 aa. head WT.pdb ATOM 1 N MET A 1 -23.707 -0.652 1… --- ## [Utilizing GROMACS Simulation Files for DNA Structure Analysis with the biobb\_dna Package](https://ask.bioexcel.eu/t/utilizing-gromacs-simulation-files-for-dna-structure-analysis-with-the-biobb-dna-package/5003)
**Author:** [@fatemeh](https://ask.bioexcel.eu/u/fatemeh)\ **Replies:** 11\ **Last updated:** [August 19, 2024, 10:41am UTC](https://ask.bioexcel.eu/t/utilizing-gromacs-simulation-files-for-dna-structure-analysis-with-the-biobb-dna-package/5003 "2024-08-19T10:41:46Z")
Hello, I would like to use biobb\_dna to analyze the DNA structure. I have used GROMACS, so I have .tpr and .xtc files. Can I use these files with biobb\_dna ? thank you in advance --- ## [Example for software feedback](https://ask.bioexcel.eu/t/example-for-software-feedback/5176)
**Author:** [@alevil](https://ask.bioexcel.eu/u/alevil)\ **Replies:** 0\ **Last updated:** [July 5, 2024, 1:18pm UTC](https://ask.bioexcel.eu/t/example-for-software-feedback/5176 "2024-07-05T13:18:25Z")
Topic: Feedback on GROMACS, HADDOCK, BioBB and PMX Feedback: write the features you would like to be implemented in the future and ideas to improve the core applications. Login to post, select the sub-category softwar…