# \#forcefield **URL:** https://gromacs.bioexcel.eu/tag/forcefield/5.md [Latest](https://gromacs.bioexcel.eu/latest.md) · [Categories](https://gromacs.bioexcel.eu/categories.md) · [Tags](https://gromacs.bioexcel.eu/tags.md) --- ## [Port LignAmb25 Force Field to GROMACS](https://gromacs.bioexcel.eu/t/port-lignamb25-force-field-to-gromacs/13642)
**Author:** [@robingarcia](https://gromacs.bioexcel.eu/u/robingarcia)\ **Replies:** 3\ **Last updated:** [September 10, 2026, 2:15pm UTC](https://gromacs.bioexcel.eu/t/port-lignamb25-force-field-to-gromacs/13642 "2026-09-10T14:15:05Z")
GROMACS version: 2026.0=nompi\_cuda\_h39c90b0\_0 GROMACS modification: No Dear community, I would like to use the LignAmb25 force field in pdb2gmx. Unfortunately, unlike CHARMM36, you can’t simply download the LignAmb25… --- ## [NPγT vs NPT for Unrestrained Membrane Equilibration Using the CHARMM36 Force Field](https://gromacs.bioexcel.eu/t/np-t-vs-npt-for-unrestrained-membrane-equilibration-using-the-charmm36-force-field/13653)
**Author:** [@xlr8](https://gromacs.bioexcel.eu/u/xlr8)\ **Replies:** 10\ **Last updated:** [August 26, 2026, 2:43pm UTC](https://gromacs.bioexcel.eu/t/np-t-vs-npt-for-unrestrained-membrane-equilibration-using-the-charmm36-force-field/13653 "2026-08-26T14:43:44Z")
GROMACS version:2025 GROMACS modification: Yes/No Here post your question Hello everyone, I am currently setting up a membrane protein simulation using the CHARMM36m force field and would appreciate some guidance reg… --- ## [Query on electrostatic treatment for slab/interface systems (2D periodicity)](https://gromacs.bioexcel.eu/t/query-on-electrostatic-treatment-for-slab-interface-systems-2d-periodicity/13679)
**Author:** [@Yihao-Zhao](https://gromacs.bioexcel.eu/u/Yihao-Zhao)\ **Replies:** 1\ **Last updated:** [August 24, 2026, 10:41am UTC](https://gromacs.bioexcel.eu/t/query-on-electrostatic-treatment-for-slab-interface-systems-2d-periodicity/13679 "2026-08-24T10:41:44Z")
GROMACS version: GROMACS modification: Yes/No Here post your question Dear GROMACS developers and users, I have a question regarding the electrostatic calculation for systems with 2D periodicity (periodic in XY, non-… --- ## [Discontinuity in bias energy function for periodic collective variables](https://gromacs.bioexcel.eu/t/discontinuity-in-bias-energy-function-for-periodic-collective-variables/13670)
**Author:** [@shaunak](https://gromacs.bioexcel.eu/u/shaunak)\ **Replies:** 4\ **Last updated:** [August 20, 2026, 4:23am UTC](https://gromacs.bioexcel.eu/t/discontinuity-in-bias-energy-function-for-periodic-collective-variables/13670 "2026-08-20T04:23:23Z")
Hi devs, I’m trying to understand how the biased simulations for techniques like umbrella sampling work in principle. When we add a bias to the potential function for, say a dihedral collective variable, U\_b(\\mathbf{x})… --- ## [Topology and force-field parameters for Rhodamine B in water](https://gromacs.bioexcel.eu/t/topology-and-force-field-parameters-for-rhodamine-b-in-water/13657)
**Author:** [@Chann](https://gromacs.bioexcel.eu/u/Chann)\ **Replies:** 0\ **Last updated:** [August 10, 2026, 11:48pm UTC](https://gromacs.bioexcel.eu/t/topology-and-force-field-parameters-for-rhodamine-b-in-water/13657 "2026-08-10T23:48:10Z")
GROMACS version: 2025.3 GROMACS modification: No Hello everyone, I am preparing an all-atom MD simulation of a single Rhodamine B molecule in explicit water. My goal is to calculate its translational diffusion coeffic… --- ## [Issue generating PFBS anion parameters with LigParGen](https://gromacs.bioexcel.eu/t/issue-generating-pfbs-anion-parameters-with-ligpargen/12633)
**Author:** [@medha](https://gromacs.bioexcel.eu/u/medha)\ **Replies:** 2\ **Last updated:** [August 5, 2026, 11:47am UTC](https://gromacs.bioexcel.eu/t/issue-generating-pfbs-anion-parameters-with-ligpargen/12633 "2026-08-05T11:47:22Z")
Hello, I am trying to generate force field parameters for the PFBS anion using LigParGen, but the server consistently fails whether I provide a PDB file or the SMILES code—it only returns an error message. I came acros… --- ## [HEAVY\_H masses in the CHARMM36m GROMACS force field](https://gromacs.bioexcel.eu/t/heavy-h-masses-in-the-charmm36m-gromacs-force-field/13626)
**Author:** [@yongwang](https://gromacs.bioexcel.eu/u/yongwang)\ **Replies:** 9\ **Last updated:** [August 5, 2026, 10:03am UTC](https://gromacs.bioexcel.eu/t/heavy-h-masses-in-the-charmm36m-gromacs-force-field/13626 "2026-08-05T10:03:07Z")
Dear GROMACS developers, I recently noticed what appears to be a potential inconsistency in the Hydrogen Mass Repartitioning (HMR) implementation of the GROMACS version of the CHARMM36 force field (downloaded from MacKe… --- ## [Constructing core shell nanoparticle](https://gromacs.bioexcel.eu/t/constructing-core-shell-nanoparticle/13643)
**Author:** [@Nostalgic](https://gromacs.bioexcel.eu/u/Nostalgic)\ **Replies:** 0\ **Last updated:** [August 4, 2026, 6:13pm UTC](https://gromacs.bioexcel.eu/t/constructing-core-shell-nanoparticle/13643 "2026-08-04T18:13:45Z")
GROMACS version: 2026.3 GROMACS modification: Yes/No Dear All, I am a beginner in GROMACS and would like to construct a core–shell nanoparticle, for example Fe₃O₄@Zr-MOF, and load it with oxaliplatin. Could anyone sug… --- ## [Parametrization of pyroglutamate](https://gromacs.bioexcel.eu/t/parametrization-of-pyroglutamate/13606)
**Author:** [@mostafagh98](https://gromacs.bioexcel.eu/u/mostafagh98)\ **Replies:** 2\ **Last updated:** [July 28, 2026, 5:29pm UTC](https://gromacs.bioexcel.eu/t/parametrization-of-pyroglutamate/13606 "2026-07-28T17:29:06Z")
GROMACS version: 2026 GROMACS modification: No Hi everyone, I am currently setting up simulations of Aβ(pE3-42) using the CHARMM36m force field in GROMACS. The N-terminal residue of this peptide is pyroglutamate (pGl… --- ## [Simulation of a dizinc metallo protein](https://gromacs.bioexcel.eu/t/simulation-of-a-dizinc-metallo-protein/9390)
**Author:** [@fatpmeireles](https://gromacs.bioexcel.eu/u/fatpmeireles)\ **Replies:** 6\ **Last updated:** [July 24, 2026, 2:16pm UTC](https://gromacs.bioexcel.eu/t/simulation-of-a-dizinc-metallo-protein/9390 "2026-07-24T14:16:11Z")
GROMACS version: 2024 GROMACS modification: Yes/No Dear users, I’d like to know if anyone has some experience simulating dizinc metalloproteins with the CHARMM force field, specifically metallo-beta-lactamases with on… --- ## [X2top not generating listed interactions correctly](https://gromacs.bioexcel.eu/t/x2top-not-generating-listed-interactions-correctly/13593)
**Author:** [@MichelePellegrino](https://gromacs.bioexcel.eu/u/MichelePellegrino)\ **Replies:** 1\ **Last updated:** [July 23, 2026, 1:17pm UTC](https://gromacs.bioexcel.eu/t/x2top-not-generating-listed-interactions-correctly/13593 "2026-07-23T13:17:21Z")
GROMACS version: 2026.1 GROMACS modification: No Hi, I am trying to generate the topology for two refrigerant molecules (1233zd and 1234ze) using gmx x2top. These are my force field files: workflow-refrigerants/examp… --- ## [How to determine b0 and kb in Zn-coordinated bond](https://gromacs.bioexcel.eu/t/how-to-determine-b0-and-kb-in-zn-coordinated-bond/13569)
**Author:** [@JoyeHye](https://gromacs.bioexcel.eu/u/JoyeHye)\ **Replies:** 0\ **Last updated:** [July 2, 2026, 10:24am UTC](https://gromacs.bioexcel.eu/t/how-to-determine-b0-and-kb-in-zn-coordinated-bond/13569 "2026-07-02T10:24:51Z")
GROMACS version: 2025.4-conda\_forge GROMACS modification: No I am processing a zinc finger protein structure, in which Zn ions form four-coordinate bonds with two Cys SG atoms and two His NE2 atoms (Cys (SG) and His (N… --- ## [IFT in CG simulation using MARTINI 3.0](https://gromacs.bioexcel.eu/t/ift-in-cg-simulation-using-martini-3-0/13522)
**Author:** [@promovr](https://gromacs.bioexcel.eu/u/promovr)\ **Replies:** 1\ **Last updated:** [June 12, 2026, 8:41am UTC](https://gromacs.bioexcel.eu/t/ift-in-cg-simulation-using-martini-3-0/13522 "2026-06-12T08:41:39Z")
GROMACS version: 2026.0 GROMACS modification: No Dear GROMACS community, I am trying to simulate an “island-type” asphaltene model using the Martini 3.0 force field. I performed the CG mapping in Materials Studio 2024… --- ## [Modified dihedral notation](https://gromacs.bioexcel.eu/t/modified-dihedral-notation/13481)
**Author:** [@mandarkulkarni](https://gromacs.bioexcel.eu/u/mandarkulkarni)\ **Replies:** 6\ **Last updated:** [June 3, 2026, 9:55am UTC](https://gromacs.bioexcel.eu/t/modified-dihedral-notation/13481 "2026-06-03T09:55:02Z")
GROMACS version: GROMACS modification: No Hi, I am working on a set of modified nucleic acids, and I need to define different dihedral parameters for the same dihedral type (e.g., OS-CT-CT-F) but for different RNA res… --- ## [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… --- ## [Covalent bound PLP to SPT (membrane bound)](https://gromacs.bioexcel.eu/t/covalent-bound-plp-to-spt-membrane-bound/13405)
**Author:** [@WoutVE](https://gromacs.bioexcel.eu/u/WoutVE)\ **Replies:** 0\ **Last updated:** [April 22, 2026, 1:18pm UTC](https://gromacs.bioexcel.eu/t/covalent-bound-plp-to-spt-membrane-bound/13405 "2026-04-22T13:18:38Z")
GROMACS version: 2024.3 GROMACS modification: No Hi, I have been wanting to simulate a membrane bound SPT complex that has a covalently linked PLP to lysine. I have found proper parameters for PLP in this study. You c… --- ## [Obtaining parameters for ligands in a nanoparticle assembly](https://gromacs.bioexcel.eu/t/obtaining-parameters-for-ligands-in-a-nanoparticle-assembly/13364)
**Author:** [@mjm91](https://gromacs.bioexcel.eu/u/mjm91)\ **Replies:** 0\ **Last updated:** [April 5, 2026, 9:32am UTC](https://gromacs.bioexcel.eu/t/obtaining-parameters-for-ligands-in-a-nanoparticle-assembly/13364 "2026-04-05T09:32:06Z")
Dear gromacs users, I am working on a simulation of a gold-nanoparticle assembly with a supramolecular complex to study host-guest encapsulation process. I prepared the gold nanoparticle assembly structure with -CH2-NH3… --- ## [Simulation of polypropylene huntite melt!](https://gromacs.bioexcel.eu/t/simulation-of-polypropylene-huntite-melt/13352)
**Author:** [@Evangelia](https://gromacs.bioexcel.eu/u/Evangelia)\ **Replies:** 0\ **Last updated:** [April 1, 2026, 11:03am UTC](https://gromacs.bioexcel.eu/t/simulation-of-polypropylene-huntite-melt/13352 "2026-04-01T11:03:10Z")
GROMACS version: GROMACS modification: Yes/No Here post your question Hello everyone, I am new to GROMACS and I am trying to build a model for an isotactic polypropylene (iPP) melt containing huntite, and later other… --- ## [PEG2000 collapsing into bilayer core in atomistic simulation (GROMOS 53A6)](https://gromacs.bioexcel.eu/t/peg2000-collapsing-into-bilayer-core-in-atomistic-simulation-gromos-53a6/13315)
**Author:** [@Anjana1](https://gromacs.bioexcel.eu/u/Anjana1)\ **Replies:** 0\ **Last updated:** [March 19, 2026, 11:00pm UTC](https://gromacs.bioexcel.eu/t/peg2000-collapsing-into-bilayer-core-in-atomistic-simulation-gromos-53a6/13315 "2026-03-19T23:00:30Z")
GROMACS version: 2018 GROMACS modification: Yes/No Hello everyone, I am performing atomistic molecular dynamics simulations of a lipid bilayer system composed of an ionizable lipid, phospholipid, cholesterol, and PEG-… --- ## [Amber FF parameters for metal binding centres](https://gromacs.bioexcel.eu/t/amber-ff-parameters-for-metal-binding-centres/2358)
**Author:** [@acnash](https://gromacs.bioexcel.eu/u/acnash)\ **Replies:** 4\ **Last updated:** [March 17, 2026, 10:41am UTC](https://gromacs.bioexcel.eu/t/amber-ff-parameters-for-metal-binding-centres/2358 "2026-03-17T10:41:58Z")
GROMACS version: 2021.2 GROMACS modification: No Dear all, I would be very grateful for an update on the latest, greatest and perhaps easiest third party tool for the parameterization of the Amber FF (packaged with Gr… --- ## [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… --- ## [Amber19SB and Amber14SB in old versions of Gromacs](https://gromacs.bioexcel.eu/t/amber19sb-and-amber14sb-in-old-versions-of-gromacs/13106)
**Author:** [@ncheron](https://gromacs.bioexcel.eu/u/ncheron)\ **Replies:** 13\ **Last updated:** [February 27, 2026, 1:54pm UTC](https://gromacs.bioexcel.eu/t/amber19sb-and-amber14sb-in-old-versions-of-gromacs/13106 "2026-02-27T13:54:10Z")
Dear all, In the 2026 release, there are new amber force fields that are available (ff14SB and ff19SB). I am wondering if they could work on old versions of Gromacs? The CMAP is available since Gromacs 2025 if I am corr… --- ## [Define ATP+mg in Amber forcefield](https://gromacs.bioexcel.eu/t/define-atp-mg-in-amber-forcefield/13237)
**Author:** [@Mobina](https://gromacs.bioexcel.eu/u/Mobina)\ **Replies:** 0\ **Last updated:** [February 23, 2026, 7:21pm UTC](https://gromacs.bioexcel.eu/t/define-atp-mg-in-amber-forcefield/13237 "2026-02-23T19:21:56Z")
GROMACS version:2025 GROMACS modification: No Hello everyone, I am using Amber99SB-ildn force field to simulate a kinase in complex with ATP and Mg. I generated the protein topology using pdb2gmx. Then created ATP topo… --- ## [CGenFF ERROR - attype warning: unknown sulfur type (SD) not supported; skipped molecule](https://gromacs.bioexcel.eu/t/cgenff-error-attype-warning-unknown-sulfur-type-sd-not-supported-skipped-molecule/10722)
**Author:** [@bee9](https://gromacs.bioexcel.eu/u/bee9)\ **Replies:** 2\ **Last updated:** [February 16, 2026, 5:55pm UTC](https://gromacs.bioexcel.eu/t/cgenff-error-attype-warning-unknown-sulfur-type-sd-not-supported-skipped-molecule/10722 "2026-02-16T17:55:26Z")
GROMACS version: GROMACS modification: Yes/No Hello everyone, I want to obtain the topology file for the ligand S-Adenosyl Methionine (SAM) (image attached). While using CGenFF, I am getting the following error. CHAR… --- ## [Amber99sb-ildn ff with Hydroxyproline](https://gromacs.bioexcel.eu/t/amber99sb-ildn-ff-with-hydroxyproline/13083)
**Author:** [@janindujk](https://gromacs.bioexcel.eu/u/janindujk)\ **Replies:** 1\ **Last updated:** [February 10, 2026, 7:59am UTC](https://gromacs.bioexcel.eu/t/amber99sb-ildn-ff-with-hydroxyproline/13083 "2026-02-10T07:59:24Z")
I am working on type 3 collagen with hyp residues. 1 N HYP A 2 2 HN1 HYP A 2 3 HN2 HYP A 2 4 CD HYP A 2 5 HD1 HYP A 2 6 HD2 HYP A 2 7 CA HYP A 2 8 HA HYP A 2 9 CB HYP A 2 10 HB… --- ## [How to build Ligand topology](https://gromacs.bioexcel.eu/t/how-to-build-ligand-topology/13142)
**Author:** [@Riya](https://gromacs.bioexcel.eu/u/Riya)\ **Replies:** 2\ **Last updated:** [February 4, 2026, 11:27am UTC](https://gromacs.bioexcel.eu/t/how-to-build-ligand-topology/13142 "2026-02-04T11:27:47Z")
GROMACS version: 2025 GROMACS modification: No Hello everyone, I am new to molecular dynamics simulations and I would like to confirm whether my procedure for building a ligand topology is correct, and how to properly… --- ## [Your Review on AMBER19sb MD in GROMACS2026](https://gromacs.bioexcel.eu/t/your-review-on-amber19sb-md-in-gromacs2026/13167)
**Author:** [@pk1997](https://gromacs.bioexcel.eu/u/pk1997)\ **Replies:** 1\ **Last updated:** [February 4, 2026, 9:05am UTC](https://gromacs.bioexcel.eu/t/your-review-on-amber19sb-md-in-gromacs2026/13167 "2026-02-04T09:05:03Z")
GROMACS version: 2026 GROMACS modification: No Hi, has anyone tried simulating with the newly ported AMBER19SB forcefield in GROMACS 2026? Apart from choosing OPC water model in pdb2gmx selection and ‘gmx solvate -cs … --- ## [How to add hydrogen atoms to the complex with correct coordinates?](https://gromacs.bioexcel.eu/t/how-to-add-hydrogen-atoms-to-the-complex-with-correct-coordinates/13136)
**Author:** [@Riggs](https://gromacs.bioexcel.eu/u/Riggs)\ **Replies:** 2\ **Last updated:** [January 23, 2026, 7:19am UTC](https://gromacs.bioexcel.eu/t/how-to-add-hydrogen-atoms-to-the-complex-with-correct-coordinates/13136 "2026-01-23T07:19:50Z")
GROMACS version:2024.06 GROMACS modification: Yes/No Here post your question I am adding hydrogen atoms to the complex containing protein, DNA and RNA, and I want to run the MD simulations with the Amber14SB forcefiel… --- ## [Tabulated nonbonded potentials in GROMACS 2026](https://gromacs.bioexcel.eu/t/tabulated-nonbonded-potentials-in-gromacs-2026/13133)
**Author:** [@Kajetan](https://gromacs.bioexcel.eu/u/Kajetan)\ **Replies:** 1\ **Last updated:** [January 21, 2026, 2:37pm UTC](https://gromacs.bioexcel.eu/t/tabulated-nonbonded-potentials-in-gromacs-2026/13133 "2026-01-21T14:37:13Z")
GROMACS version: 2026 GROMACS modification: No The GROMACS 2026 documentation explicitly mentions tabulated interaction functions, without stating that this functionality is deprecated or planned for removal, as was in… --- ## [Charge precision in topology files: parsing behaviour and validation tolerance](https://gromacs.bioexcel.eu/t/charge-precision-in-topology-files-parsing-behaviour-and-validation-tolerance/13103)
**Author:** [@tbde](https://gromacs.bioexcel.eu/u/tbde)\ **Replies:** 5\ **Last updated:** [January 21, 2026, 11:27am UTC](https://gromacs.bioexcel.eu/t/charge-precision-in-topology-files-parsing-behaviour-and-validation-tolerance/13103 "2026-01-21T11:27:58Z")
GROMACS version: 2020.7 GROMACS modification: No Hello, I’m working with a coarse-grained model that uses fractional charges (1/3 to 16 sig. figs.) distributed across polymer chains, with the terminal bead carrying th… [Next page](https://gromacs.bioexcel.eu/tag/forcefield/5.md?match_all_tags=true&page=1&tags%5B%5D=forcefield)