# Third party tools and files **URL:** https://gromacs.bioexcel.eu/c/third-party-tools-and-files/8.md [Latest](https://gromacs.bioexcel.eu/latest.md) · [Categories](https://gromacs.bioexcel.eu/categories.md) · [Tags](https://gromacs.bioexcel.eu/tags.md) --- ## [About the Third party tools and files category](https://gromacs.bioexcel.eu/t/about-the-third-party-tools-and-files-category/816)
**Author:** [@avilla](https://gromacs.bioexcel.eu/u/avilla)\ **Replies:** 0\ **Last updated:** [September 15, 2020, 3:15pm UTC](https://gromacs.bioexcel.eu/t/about-the-third-party-tools-and-files-category/816 "2020-09-15T15:15:17Z")
Here you find third party tools and files (e.i force fields database, structure file, topology file and so on) useful for the GROMACS community. You can create a new post to describe tools and files, useful for the GROMA… --- ## [DSSNA — nucleic acids secondary/tertiary structure analysis tool for MD trajectories](https://gromacs.bioexcel.eu/t/dssna-nucleic-acids-secondary-tertiary-structure-analysis-tool-for-md-trajectories/13745)
**Author:** [@Sorcerer](https://gromacs.bioexcel.eu/u/Sorcerer)\ **Replies:** 2\ **Last updated:** [October 7, 2026, 7:35am UTC](https://gromacs.bioexcel.eu/t/dssna-nucleic-acids-secondary-tertiary-structure-analysis-tool-for-md-trajectories/13745 "2026-10-07T07:35:18Z")
Dear GROMACS community, I would like to share a tool that may be of interest to those simulating DNA and RNA systems. DSSNA (Define Spatial Structure of Nucleic Acids) is an algorithm for automatic assignment of second… --- ## [hbonds autocorrelation using GROMACS](https://gromacs.bioexcel.eu/t/hbonds-autocorrelation-using-gromacs/13660)
**Author:** [@askforarun](https://gromacs.bioexcel.eu/u/askforarun)\ **Replies:** 0\ **Last updated:** [August 11, 2026, 5:20pm UTC](https://gromacs.bioexcel.eu/t/hbonds-autocorrelation-using-gromacs/13660 "2026-08-11T17:20:19Z")
Python tool for calculating hydrogen-bond autocorrelation functions from GROMACS gmx hbond -pf output. It calculates both intermittent and continuous hydrogen-bond autocorrelation functions and supports user-defined lag … --- ## [\[TOOL\] 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, … --- ## [New atomipy online molecular builder for inorganic/geochemical based systems](https://gromacs.bioexcel.eu/t/new-atomipy-online-molecular-builder-for-inorganic-geochemical-based-systems/13416)
**Author:** [@mholmboe](https://gromacs.bioexcel.eu/u/mholmboe)\ **Replies:** 0\ **Last updated:** [April 26, 2026, 10:27am UTC](https://gromacs.bioexcel.eu/t/new-atomipy-online-molecular-builder-for-inorganic-geochemical-based-systems/13416 "2026-04-26T10:27:26Z")
I have created a simple React flow online server running the atomipy package (Atomistic Topology Operations in MATLAB - but In Python) at www.atomipy.io, which can be used for building and analyzing in particular inorgan… --- ## [\`opc.gro\` available on GitHub](https://gromacs.bioexcel.eu/t/opc-gro-available-on-github/13380)
**Author:** [@Ernest\_NH\_Ho](https://gromacs.bioexcel.eu/u/Ernest_NH_Ho)\ **Replies:** 1\ **Last updated:** [April 13, 2026, 11:20am UTC](https://gromacs.bioexcel.eu/t/opc-gro-available-on-github/13380 "2026-04-13T11:20:38Z")
I recently installed the 2026.1 version. Initially, I chose opc water model, but I couldn’t find any opc.gro, so I used tip4p.gro. However, it occasionally returned a “Not enough replaceable solvent molecules”. Clearly… --- ## [Align\_vector\_to\_box\_axis.py - A Python script to align a protein to one of the three axes](https://gromacs.bioexcel.eu/t/align-vector-to-box-axis-py-a-python-script-to-align-a-protein-to-one-of-the-three-axes/13353)
**Author:** [@hansdewinter](https://gromacs.bioexcel.eu/u/hansdewinter)\ **Replies:** 0\ **Last updated:** [April 1, 2026, 3:15pm UTC](https://gromacs.bioexcel.eu/t/align-vector-to-box-axis-py-a-python-script-to-align-a-protein-to-one-of-the-three-axes/13353 "2026-04-01T15:15:12Z")
The align\_vector\_to\_box\_axis.py Python3 script has been written to align a user-definable vector, provided by two groups defined in the index file, along one of the three axes (x, y, or z). The tool takes as input a .gro… --- ## [plotXVG: Batch Generation of Publication-Quality Graphs from GROMACS Output](https://gromacs.bioexcel.eu/t/plotxvg-batch-generation-of-publication-quality-graphs-from-gromacs-output/13343)
**Author:** [@dspoel](https://gromacs.bioexcel.eu/u/dspoel)\ **Replies:** 0\ **Last updated:** [March 30, 2026, 12:21pm UTC](https://gromacs.bioexcel.eu/t/plotxvg-batch-generation-of-publication-quality-graphs-from-gromacs-output/13343 "2026-03-30T12:21:50Z")
Dear all, I am happy to announce the availability of plotxvg, a script based on matplotlib that will allow you to plot most xvg files produced by GROMACS from the command line, or using your own Python pipeline, directl… --- ## [Newest CHARMM36 port for GROMACS](https://gromacs.bioexcel.eu/t/newest-charmm36-port-for-gromacs/868)
**Author:** [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Replies:** 39\ **Last updated:** [March 5, 2026, 1:41am UTC](https://gromacs.bioexcel.eu/t/newest-charmm36-port-for-gromacs/868 "2026-03-05T01:41:57Z")
We are pleased to announce an updated port of the CHARMM36 force field for GROMACS, available at http://mackerell.umaryland.edu/charmm\_ff.shtml#gromacs The July 2020 release corresponds to the annual update to the CHAR… --- ## [LAMMPS TO GROMACS ](https://gromacs.bioexcel.eu/t/lammps-to-gromacs/13229)
**Author:** [@askforarun](https://gromacs.bioexcel.eu/u/askforarun)\ **Replies:** 0\ **Last updated:** [February 18, 2026, 10:34am UTC](https://gromacs.bioexcel.eu/t/lammps-to-gromacs/13229 "2026-02-18T10:34:37Z")
A lightweight Python utility to convert LAMMPS structures into GROMACS .gro format. The tool includes residue naming support to improve topology handling and interoperability between simulation workflows. Designed for si… --- ## [gmx\_MMPBSA: a new tool aiming to perform end-state free energy calculations with GROMACS files](https://gromacs.bioexcel.eu/t/gmx-mmpbsa-a-new-tool-aiming-to-perform-end-state-free-energy-calculations-with-gromacs-files/2338)
**Author:** [@mevaldes](https://gromacs.bioexcel.eu/u/mevaldes)\ **Replies:** 2\ **Last updated:** [January 14, 2026, 6:32pm UTC](https://gromacs.bioexcel.eu/t/gmx-mmpbsa-a-new-tool-aiming-to-perform-end-state-free-energy-calculations-with-gromacs-files/2338 "2026-01-14T18:32:13Z")
Brief description of tools/files: gmx\_MMPBSA (Getting started - gmx\_MMPBSA Documentation) is a new tool based on AMBER’s MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files. It works with a… --- ## [Supporting CIF Format in GROMACS](https://gromacs.bioexcel.eu/t/supporting-cif-format-in-gromacs/7244)
**Author:** [@whyprophecy](https://gromacs.bioexcel.eu/u/whyprophecy)\ **Replies:** 3\ **Last updated:** [November 13, 2025, 5:32am UTC](https://gromacs.bioexcel.eu/t/supporting-cif-format-in-gromacs/7244 "2025-11-13T05:32:22Z")
We modified the source codes of GROMACS, which enables it to support the CIF format structure files as direct input and subsequently generate molecular topology files. For very large protein complexes lacking PDB-format … --- ## [x2top for MINFF](https://gromacs.bioexcel.eu/t/x2top-for-minff/12722)
**Author:** [@mholmboe](https://gromacs.bioexcel.eu/u/mholmboe)\ **Replies:** 0\ **Last updated:** [October 2, 2025, 6:23am UTC](https://gromacs.bioexcel.eu/t/x2top-for-minff/12722 "2025-10-02T06:23:48Z")
I have modified the gmx x2top tool so that it can also be used to generate Gromacs .top or .itp topology files for the MINFF forcefield (for oxides/hydroxides and many (clay)minerals), using simple .n2t files now availab… --- ## [gmx\_ffconv: A Fast, User-Friendly Semi-Automated All-Atom Force Field Converter for GROMACS](https://gromacs.bioexcel.eu/t/gmx-ffconv-a-fast-user-friendly-semi-automated-all-atom-force-field-converter-for-gromacs/12672)
**Author:** [@Jassu](https://gromacs.bioexcel.eu/u/Jassu)\ **Replies:** 0\ **Last updated:** [September 21, 2025, 4:23pm UTC](https://gromacs.bioexcel.eu/t/gmx-ffconv-a-fast-user-friendly-semi-automated-all-atom-force-field-converter-for-gromacs/12672 "2025-09-21T16:23:04Z")
Dear All, I’m happy to announce that gmx\_ffconv is now officially out. gmx\_ffconv is a force field agnostic, semi-automated force field converter for GROMACS. It enables users to easily convert a system between two all… --- ## [gmx\_clusterByFeatures - Features-based conformational clustering from MD Simulations](https://gromacs.bioexcel.eu/t/gmx-clusterbyfeatures-features-based-conformational-clustering-from-md-simulations/12336)
**Author:** [@rjdkmrniper](https://gromacs.bioexcel.eu/u/rjdkmrniper)\ **Replies:** 0\ **Last updated:** [July 7, 2025, 3:08pm UTC](https://gromacs.bioexcel.eu/t/gmx-clusterbyfeatures-features-based-conformational-clustering-from-md-simulations/12336 "2025-07-07T15:08:28Z")
I have developed a user-friendly tool to perform feature-based conformational clustering from MD simulations. It is a package containing several sub-commands and some of the commands are very similar to the GROMACS Analy… --- ## [g\_mmpbsa update for latest GROMACS](https://gromacs.bioexcel.eu/t/g-mmpbsa-update-for-latest-gromacs/12198)
**Author:** [@rjdkmrniper](https://gromacs.bioexcel.eu/u/rjdkmrniper)\ **Replies:** 0\ **Last updated:** [June 4, 2025, 5:02pm UTC](https://gromacs.bioexcel.eu/t/g-mmpbsa-update-for-latest-gromacs/12198 "2025-06-04T17:02:52Z")
Hi All, Thank you all for using g\_mmpbsa extensively. We introduced g\_mmpbsa almost 11 years ago to perform MM/PBSA binding energy calculations using GROMACS, earning over 4000 citations since then. Despite not updatin… --- ## [gorder: Comprehensive tool for calculating lipid order parameters from molecular simulations](https://gromacs.bioexcel.eu/t/gorder-comprehensive-tool-for-calculating-lipid-order-parameters-from-molecular-simulations/12070)
**Author:** [@Ladme](https://gromacs.bioexcel.eu/u/Ladme)\ **Replies:** 0\ **Last updated:** [May 12, 2025, 6:36pm UTC](https://gromacs.bioexcel.eu/t/gorder-comprehensive-tool-for-calculating-lipid-order-parameters-from-molecular-simulations/12070 "2025-05-12T18:36:48Z")
Hello, everyone, being unsatisfied with the misuse of gmx order, we have developed a tool called gorder for calculating lipid order parameters from atomistic, united-atom, and coarse-grained Gromacs simulations. It’s co… --- ## [Online server for MINFF and CLAYFF topologies](https://gromacs.bioexcel.eu/t/online-server-for-minff-and-clayff-topologies/11905)
**Author:** [@mholmboe](https://gromacs.bioexcel.eu/u/mholmboe)\ **Replies:** 0\ **Last updated:** [April 10, 2025, 7:19am UTC](https://gromacs.bioexcel.eu/t/online-server-for-minff-and-clayff-topologies/11905 "2025-04-10T07:19:34Z")
Hi, I have setup a simple online server running our new lightweight atomipy package (Atomistic Topology Operations in Matlab - but In Python) at www.atomipy.io, which can generate .itp files for minerals according to th… --- ## [MINFF: a new family of forcefields for minerals](https://gromacs.bioexcel.eu/t/minff-a-new-family-of-forcefields-for-minerals/10735)
**Author:** [@mholmboe](https://gromacs.bioexcel.eu/u/mholmboe)\ **Replies:** 0\ **Last updated:** [December 5, 2024, 5:09pm UTC](https://gromacs.bioexcel.eu/t/minff-a-new-family-of-forcefields-for-minerals/10735 "2024-12-05T17:09:31Z")
MINFF is a newly developed molecular dynamics (MD) forcefield designed for simulating Si, Al, Fe, Mg, Ca, Ti, Li, F containing oxides and hydroxides, including hydrated clay minerals and zeolites. MINFF incorporates ang… --- ## [dRama: Differential Ramachandran Plot as a Tool to Analyze Subtle Changes in Protein Structure](https://gromacs.bioexcel.eu/t/drama-differential-ramachandran-plot-as-a-tool-to-analyze-subtle-changes-in-protein-structure/10636)
**Author:** [@Pbatys](https://gromacs.bioexcel.eu/u/Pbatys)\ **Replies:** 0\ **Last updated:** [November 26, 2024, 9:55am UTC](https://gromacs.bioexcel.eu/t/drama-differential-ramachandran-plot-as-a-tool-to-analyze-subtle-changes-in-protein-structure/10636 "2024-11-26T09:55:37Z")
Brief description of tools/files: Ramachandran plot is often used to analyze the MD simulation results. The problem with classical Ramachandran plot, however, is that it becomes gradually indecipherable at a high number… --- ## [amber14sb\_OL15.ff correction in Dihedrals](https://gromacs.bioexcel.eu/t/amber14sb-ol15-ff-correction-in-dihedrals/5497)
**Author:** [@Stanislav\_Bachurin](https://gromacs.bioexcel.eu/u/Stanislav_Bachurin)\ **Replies:** 2\ **Last updated:** [April 25, 2024, 2:05am UTC](https://gromacs.bioexcel.eu/t/amber14sb-ol15-ff-correction-in-dihedrals/5497 "2024-04-25T02:05:34Z")
Dear collegues! Right now I revealed that there is a mistake in amber14sb\_OL15.ff. File ffbonded.itp should be modified in lines 801-804. Instead of 801 CT CV CC NA 4 180.00 4.60240 2 802 C… --- ## [GenTopo: A python tool kit for generating gromacs topology template](https://gromacs.bioexcel.eu/t/gentopo-a-python-tool-kit-for-generating-gromacs-topology-template/2285)
**Author:** [@Masrul](https://gromacs.bioexcel.eu/u/Masrul)\ **Replies:** 1\ **Last updated:** [April 4, 2024, 2:49pm UTC](https://gromacs.bioexcel.eu/t/gentopo-a-python-tool-kit-for-generating-gromacs-topology-template/2285 "2024-04-04T14:49:29Z")
GenTopo: A python toolkit for generating gromacs topology template. Source Code link: GitHub - masrul/GenTopo: Gromacs topology template generator Description For non-standard Force-field (which cannot be invoked throug… --- ## [PolySMart: a general coarse-grained molecular dynamics polymerization scheme](https://gromacs.bioexcel.eu/t/polysmart-a-general-coarse-grained-molecular-dynamics-polymerization-scheme/8393)
**Author:** [@mohammadm](https://gromacs.bioexcel.eu/u/mohammadm)\ **Replies:** 0\ **Last updated:** [February 21, 2024, 12:33pm UTC](https://gromacs.bioexcel.eu/t/polysmart-a-general-coarse-grained-molecular-dynamics-polymerization-scheme/8393 "2024-02-21T12:33:58Z")
PolySMart is a python package which is designed to perform a reactive MD simulation in GROMACS MD package using MARTINI coarse-grain forcefield. It is specially designed to perform polymerization and crosslinking process… --- ## [Visual Interactive Analysis of Molecular Dynamics (VIAMD)](https://gromacs.bioexcel.eu/t/visual-interactive-analysis-of-molecular-dynamics-viamd/7796)
**Author:** [@mathieulinares](https://gromacs.bioexcel.eu/u/mathieulinares)\ **Replies:** 0\ **Last updated:** [December 5, 2023, 1:10pm UTC](https://gromacs.bioexcel.eu/t/visual-interactive-analysis-of-molecular-dynamics-viamd/7796 "2023-12-05T13:10:50Z")
Brief description of the tool: VIAMD (Visual Interactive Analysis of Molecular Dynamics) is an open-source software designed to facilitate molecular dynamics (MD) analysis. It simplifies the complexities associated with… --- ## [Atom: a MATLAB library for creating discrete or periodic systems and topologies (for Gromacs)](https://gromacs.bioexcel.eu/t/atom-a-matlab-library-for-creating-discrete-or-periodic-systems-and-topologies-for-gromacs/2118)
**Author:** [@mholmboe](https://gromacs.bioexcel.eu/u/mholmboe)\ **Replies:** 1\ **Last updated:** [November 12, 2023, 12:42pm UTC](https://gromacs.bioexcel.eu/t/atom-a-matlab-library-for-creating-discrete-or-periodic-systems-and-topologies-for-gromacs/2118 "2023-11-12T12:42:11Z")
The purpose of the atom MATLAB library (\>100 functions) is to automate and enable construction (adding solutes, solvent molecules without molecular overlap) of especially solvated inorganic multicomponent molecular syste… --- ## [polyGraft: A Program for Molecular Structure and Topology Generation of Polymer-Grafted Hybrid Nanos](https://gromacs.bioexcel.eu/t/polygraft-a-program-for-molecular-structure-and-topology-generation-of-polymer-grafted-hybrid-nanos/7087)
**Author:** [@nano](https://gromacs.bioexcel.eu/u/nano)\ **Replies:** 0\ **Last updated:** [August 27, 2023, 6:28pm UTC](https://gromacs.bioexcel.eu/t/polygraft-a-program-for-molecular-structure-and-topology-generation-of-polymer-grafted-hybrid-nanos/7087 "2023-08-27T18:28:59Z")
Brief description of tools/files: A general, flexible, and easy-to-use Python program for automated generation of molecular structure and topology of polymer-grafted hybrid materials for MD simulations purposes, ranging … --- ## [ComplexMixtures.jl: Investigating the structure of solutions of complex-shaped molecules](https://gromacs.bioexcel.eu/t/complexmixtures-jl-investigating-the-structure-of-solutions-of-complex-shaped-molecules/5613)
**Author:** [@lmiq](https://gromacs.bioexcel.eu/u/lmiq)\ **Replies:** 1\ **Last updated:** [June 22, 2023, 7:27pm UTC](https://gromacs.bioexcel.eu/t/complexmixtures-jl-investigating-the-structure-of-solutions-of-complex-shaped-molecules/5613 "2023-06-22T19:27:38Z")
ComplexMixtures is a package to study the solute and solvent interactions of mixtures of molecules of complex shape. Conventional radial distribution functions are not appropriate to represent the structure of a solvent … --- ## [Adding an extra input for electric field in mdp files](https://gromacs.bioexcel.eu/t/adding-an-extra-input-for-electric-field-in-mdp-files/6511)
**Author:** [@SongZG](https://gromacs.bioexcel.eu/u/SongZG)\ **Replies:** 0\ **Last updated:** [May 29, 2023, 3:13pm UTC](https://gromacs.bioexcel.eu/t/adding-an-extra-input-for-electric-field-in-mdp-files/6511 "2023-05-29T15:13:10Z")
I’m an undergraduate student from Peking University. In my current work, I found it necessary to add two electric fields in one dimension at the same time, so I made this plugin. Hopefully it will help other people if th… --- ## [Announcing gmxapi 0.2 Python package](https://gromacs.bioexcel.eu/t/announcing-gmxapi-0-2-python-package/1720)
**Author:** [@ericirrgang](https://gromacs.bioexcel.eu/u/ericirrgang)\ **Replies:** 7\ **Last updated:** [March 10, 2023, 2:26pm UTC](https://gromacs.bioexcel.eu/t/announcing-gmxapi-0-2-python-package/1720 "2023-03-10T14:26:22Z")
Good news, everyone! The gmxapi 0.2 Python package is available for GROMACS 2021, and works best with the brand new release of GROMACS 2021.1. After activating your new GROMACS installation ("source"ing your GMXRC), you… --- ## [FixBox: a tool to fix broken systems due to PBCs](https://gromacs.bioexcel.eu/t/fixbox-a-tool-to-fix-broken-systems-due-to-pbcs/5514)
**Author:** [@antonio.baptista](https://gromacs.bioexcel.eu/u/antonio.baptista)\ **Replies:** 0\ **Last updated:** [December 30, 2022, 9:52pm UTC](https://gromacs.bioexcel.eu/t/fixbox-a-tool-to-fix-broken-systems-due-to-pbcs/5514 "2022-12-30T21:52:56Z")
Dear all, We have recently made available a method to fix systems which were broken due to PBCs, named FixBox. Although PBCs are a standard and well-understood feature of molecular simulations, we all know how they can … [Next page](https://gromacs.bioexcel.eu/c/third-party-tools-and-files/8.md?page=1)