# Latest **URL:** https://gromacs.bioexcel.eu/latest.md [Latest](https://gromacs.bioexcel.eu/latest.md) · [Categories](https://gromacs.bioexcel.eu/categories.md) · [Tags](https://gromacs.bioexcel.eu/tags.md) --- ## [Addition of AMBER OL3 Force field in GROMACS](https://gromacs.bioexcel.eu/t/addition-of-amber-ol3-force-field-in-gromacs/13726)
**Author:** [@Nainsybaghel](https://gromacs.bioexcel.eu/u/Nainsybaghel)\ **Replies:** 1\ **Last updated:** [September 22, 2026, 7:47pm UTC](https://gromacs.bioexcel.eu/t/addition-of-amber-ol3-force-field-in-gromacs/13726 "2026-09-22T19:47:35Z")
GROMACS version: GROMACS modification: Yes/No Here post your question Command line: gmx pdb2gmx -f 1AKI\_clean.pdb -o 1AKI\_processed.gro -water tip3p Output: Select the Force Field: From ‘/usr/local/gromacs/share/g… --- ## [GROMACS hydrogen-bond analysis question](https://gromacs.bioexcel.eu/t/gromacs-hydrogen-bond-analysis-question/13731)
**Author:** [@Bookworm](https://gromacs.bioexcel.eu/u/Bookworm)\ **Replies:** 1\ **Last updated:** [September 22, 2026, 3:38pm UTC](https://gromacs.bioexcel.eu/t/gromacs-hydrogen-bond-analysis-question/13731 "2026-09-22T15:38:49Z")
GROMACS version: 2023.3 GROMACS modification: No Hi GROMACS community, I would like to use the GROMACS hydrogen-bond analysis tools to calculate the number of hydrogen bonds involving water in my cellulose trajectory.… --- ## [Advice on High Penalty in CGenff generated topology](https://gromacs.bioexcel.eu/t/advice-on-high-penalty-in-cgenff-generated-topology/13730)
**Author:** [@Asha1](https://gromacs.bioexcel.eu/u/Asha1)\ **Replies:** 0\ **Last updated:** [September 20, 2026, 8:59am UTC](https://gromacs.bioexcel.eu/t/advice-on-high-penalty-in-cgenff-generated-topology/13730 "2026-09-20T08:59:46Z")
GROMACS modification: Yes/No Hello Everyone, I have been trying parameterize a small part of a bigger molecule(91 atoms), which have a charge penalty of 25 and dihedral penalty of 45. I understand that these relativel… --- ## [Technical review meeting for GPU Virtual Sites](https://gromacs.bioexcel.eu/t/technical-review-meeting-for-gpu-virtual-sites/13697)
**Author:** [@lmullender](https://gromacs.bioexcel.eu/u/lmullender)\ **Replies:** 6\ **Last updated:** [September 16, 2026, 2:40pm UTC](https://gromacs.bioexcel.eu/t/technical-review-meeting-for-gpu-virtual-sites/13697 "2026-09-16T14:40:13Z")
I have been doing some work in the recent months regarding support for virtual sites with GPU-resident update. I’ve broken the change up into several parts, with the tracking issue at #5613: Supporting triangle constr… --- ## [PBCs in a slightly complex system](https://gromacs.bioexcel.eu/t/pbcs-in-a-slightly-complex-system/13711)
**Author:** [@Jameel9](https://gromacs.bioexcel.eu/u/Jameel9)\ **Replies:** 7\ **Last updated:** [September 15, 2026, 9:35am UTC](https://gromacs.bioexcel.eu/t/pbcs-in-a-slightly-complex-system/13711 "2026-09-15T09:35:56Z")
Hi everyone, I have a system made up of: Two protein chains (not interacting, that was the purpose of the simulation to see if they do). ~ 100 molecules of hexanediol. water and ions. after the simulatioin is complet… --- ## [Inconsistent shifts](https://gromacs.bioexcel.eu/t/inconsistent-shifts/756)
**Author:** [@rcrehuet](https://gromacs.bioexcel.eu/u/rcrehuet)\ **Replies:** 3\ **Last updated:** [September 14, 2026, 9:49am UTC](https://gromacs.bioexcel.eu/t/inconsistent-shifts/756 "2026-09-14T09:49:46Z")
GROMACS version: 2019.4 GROMACS modification: Yes with plumed I have performed an MD run. The simulation has run smoothly without errors or warnings about inconsistent shifts (though it is not finished yet, as it stopp… --- ## [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… --- ## [9th September, GROMACS quartely planning meeting at 12:30 CEST](https://gromacs.bioexcel.eu/t/9th-september-gromacs-quartely-planning-meeting-at-12-30-cest/13686)
**Author:** [@avilla](https://gromacs.bioexcel.eu/u/avilla)\ **Replies:** 2\ **Last updated:** [September 9, 2026, 6:29am UTC](https://gromacs.bioexcel.eu/t/9th-september-gromacs-quartely-planning-meeting-at-12-30-cest/13686 "2026-09-09T06:29:45Z")
Hi, Next planning meeting is 9th September, starting from 12:30 CEST (new starting time) in hydrid format. Aim: to provide an overview on the planned and future development effort on GROMACS, to build synergy between d… --- ## [SAM co-factor with CHARMM force field for GROMACS silmualtion](https://gromacs.bioexcel.eu/t/sam-co-factor-with-charmm-force-field-for-gromacs-silmualtion/10511)
**Author:** [@Gabbi](https://gromacs.bioexcel.eu/u/Gabbi)\ **Replies:** 14\ **Last updated:** [September 8, 2026, 6:45pm UTC](https://gromacs.bioexcel.eu/t/sam-co-factor-with-charmm-force-field-for-gromacs-silmualtion/10511 "2026-09-08T18:45:21Z")
Hello All, Following the GROMACS tutotial on Protein-ligand complex, I am trying to simulate a protein having SAM as one of its ligands using the CHARMM force field. All my attempts to get the topology file for SAM fai… --- ## [Unable to select specific chains (A/B) for a dimer in v2024.3](https://gromacs.bioexcel.eu/t/unable-to-select-specific-chains-a-b-for-a-dimer-in-v2024-3/13700)
**Author:** [@athiras](https://gromacs.bioexcel.eu/u/athiras)\ **Replies:** 6\ **Last updated:** [September 8, 2026, 9:29am UTC](https://gromacs.bioexcel.eu/t/unable-to-select-specific-chains-a-b-for-a-dimer-in-v2024-3/13700 "2026-09-08T09:29:55Z")
GROMACS version: 2024.3 Hi everyone, I am trying to create an index group for the binding pocket of a dimer using GROMACS 2024.3. The pocket consists of a few specific residues. When attempting to select the atoms, GR… --- ## [Having issue with gmx SASA giving values of 0 for specific protein](https://gromacs.bioexcel.eu/t/having-issue-with-gmx-sasa-giving-values-of-0-for-specific-protein/13709)
**Author:** [@dwat223](https://gromacs.bioexcel.eu/u/dwat223)\ **Replies:** 0\ **Last updated:** [September 8, 2026, 12:08am UTC](https://gromacs.bioexcel.eu/t/having-issue-with-gmx-sasa-giving-values-of-0-for-specific-protein/13709 "2026-09-08T00:08:31Z")
GROMACS version: 2025.2-foss-2023a-cuda-12.5.0-hybrid GROMACS modification: No Hi, I’m doing some work and it was suggested that I use gmx sasa to calculate the SASA of some binidng sites. I’m having issue with on part… --- ## [Gmx dssp gives wrong secondary structure results](https://gromacs.bioexcel.eu/t/gmx-dssp-gives-wrong-secondary-structure-results/8559)
**Author:** [@THFKevin](https://gromacs.bioexcel.eu/u/THFKevin)\ **Replies:** 6\ **Last updated:** [September 7, 2026, 2:49pm UTC](https://gromacs.bioexcel.eu/t/gmx-dssp-gives-wrong-secondary-structure-results/8559 "2026-09-07T14:49:14Z")
GROMACS version: 2024.1 GROMACS modification: No Hi everyone, I’m using the current GROMACS version that contained a new “dssp” command and removed the old “do\_dssp”. However, when I was trying to use the following co… --- ## [How can I fix a "bi-layer" during an NPT simulation?](https://gromacs.bioexcel.eu/t/how-can-i-fix-a-bi-layer-during-an-npt-simulation/13702)
**Author:** [@Aurora](https://gromacs.bioexcel.eu/u/Aurora)\ **Replies:** 3\ **Last updated:** [September 7, 2026, 12:00pm UTC](https://gromacs.bioexcel.eu/t/how-can-i-fix-a-bi-layer-during-an-npt-simulation/13702 "2026-09-07T12:00:23Z")
GROMACS version: 2025.3 Dear all, My name is Aurora Fatiga, and I work at CNR-ITM (Rende, Cosenza, Italy). I’m having some issues with GROMACS; I’ll explain my question. I would like to simulate, using GROMACS, a sys… --- ## [Does the Ewald3D-C long-range correction include a virial contribution?](https://gromacs.bioexcel.eu/t/does-the-ewald3d-c-long-range-correction-include-a-virial-contribution/13708)
**Author:** [@Yihao-Zhao](https://gromacs.bioexcel.eu/u/Yihao-Zhao)\ **Replies:** 2\ **Last updated:** [September 4, 2026, 12:47pm UTC](https://gromacs.bioexcel.eu/t/does-the-ewald3d-c-long-range-correction-include-a-virial-contribution/13708 "2026-09-04T12:47:50Z")
GROMACS version: gromacs-2025.1.Install GROMACS modification: Yes/No Here post your question Dear GROMACS developers and community, I am using Ewald3D-C for simulations of interfacial systems and would like to know w… --- ## [Using GROMACS and PLUMED to do a metadynamics simulations](https://gromacs.bioexcel.eu/t/using-gromacs-and-plumed-to-do-a-metadynamics-simulations/13689)
**Author:** [@Vero\_MH](https://gromacs.bioexcel.eu/u/Vero_MH)\ **Replies:** 1\ **Last updated:** [September 2, 2026, 9:44pm UTC](https://gromacs.bioexcel.eu/t/using-gromacs-and-plumed-to-do-a-metadynamics-simulations/13689 "2026-09-02T21:44:53Z")
GROMACS version: module load GROMACS/2024.4-foss-2023b-CUDA-12.4.0-PLUMED-2.9.2 GROMACS modification: No Hi everyone I’m trying to perform a metadynamics simulation with plumed and compare the differences in the prote… --- ## [PBC Box Failing to Expand to Input .gro File Parameters + Unwanted Position Restrained Protein](https://gromacs.bioexcel.eu/t/pbc-box-failing-to-expand-to-input-gro-file-parameters-unwanted-position-restrained-protein/12152)
**Author:** [@kbwarren](https://gromacs.bioexcel.eu/u/kbwarren)\ **Replies:** 3\ **Last updated:** [September 2, 2026, 7:51pm UTC](https://gromacs.bioexcel.eu/t/pbc-box-failing-to-expand-to-input-gro-file-parameters-unwanted-position-restrained-protein/12152 "2026-09-02T19:51:32Z")
GROMACS version: 2024.4 GROMACS modification: No Hi all, Just posting to this forum because after running a triplicate of coarse-grain lipid bilayer systems with added proteins, I was surprised with very uncharacteris… --- ## [Gromacs for Windows on Arm Architecture for Copilot+PC](https://gromacs.bioexcel.eu/t/gromacs-for-windows-on-arm-architecture-for-copilot-pc/13579)
**Author:** [@huba30](https://gromacs.bioexcel.eu/u/huba30)\ **Replies:** 6\ **Last updated:** [September 2, 2026, 1:45pm UTC](https://gromacs.bioexcel.eu/t/gromacs-for-windows-on-arm-architecture-for-copilot-pc/13579 "2026-09-02T13:45:07Z")
I 'm looking forward to knowing if GROMACS is compatible with Arm Architecture for Copilot+ PC laptops running on Windows on Arm? --- ## [Hydrogen Mass Repartitioning-Help](https://gromacs.bioexcel.eu/t/hydrogen-mass-repartitioning-help/13699)
**Author:** [@Ligand1](https://gromacs.bioexcel.eu/u/Ligand1)\ **Replies:** 1\ **Last updated:** [September 2, 2026, 8:20am UTC](https://gromacs.bioexcel.eu/t/hydrogen-mass-repartitioning-help/13699 "2026-09-02T08:20:16Z")
GROMACS version: 2026.0 GROMACS modification: No Hi everyone…I am trying to run a MD simulation on very large membrane protein complex that is basically embedded in a POPC bilayer. The system is solvated with water mol… --- ## [Solvent accessible surface area calculation in GROMACS](https://gromacs.bioexcel.eu/t/solvent-accessible-surface-area-calculation-in-gromacs/13698)
**Author:** [@Nainsybaghel](https://gromacs.bioexcel.eu/u/Nainsybaghel)\ **Replies:** 2\ **Last updated:** [September 2, 2026, 4:50am UTC](https://gromacs.bioexcel.eu/t/solvent-accessible-surface-area-calculation-in-gromacs/13698 "2026-09-02T04:50:29Z")
GROMACS version: GROMACS modification: Yes/No Here, post your question I want to know the formula and algorithm behind SASA calculation in GROMACS. I checked the GROMACS formula cite ( Index of /current/reference-man… --- ## [Constant Electric Field and Membrane Voltage in GROMACS](https://gromacs.bioexcel.eu/t/constant-electric-field-and-membrane-voltage-in-gromacs/13695)
**Author:** [@Nikke](https://gromacs.bioexcel.eu/u/Nikke)\ **Replies:** 1\ **Last updated:** [September 1, 2026, 2:21pm UTC](https://gromacs.bioexcel.eu/t/constant-electric-field-and-membrane-voltage-in-gromacs/13695 "2026-09-01T14:21:39Z")
Dear GROMACS developers and users, I would like to ask for clarification regarding the interpretation of a constant electric field applied to a membrane system using electric-field-z in GROMACS, particularly how the cor… --- ## [GROMACS 2025.5 patch release available](https://gromacs.bioexcel.eu/t/gromacs-2025-5-patch-release-available/13696)
**Author:** [@mumairsadiq](https://gromacs.bioexcel.eu/u/mumairsadiq)\ **Replies:** 0\ **Last updated:** [August 31, 2026, 2:24pm UTC](https://gromacs.bioexcel.eu/t/gromacs-2025-5-patch-release-available/13696 "2026-08-31T14:24:33Z")
Hi, GROMACS users! The official release of GROMACS 2025.5 is available! This 5th patch release fixes several issues found since the previous release of the 2025 series. We encourage all users of the 2025 series to upd… --- ## [Low GROMACS Performance on RTX 5090 Workstation](https://gromacs.bioexcel.eu/t/low-gromacs-performance-on-rtx-5090-workstation/13586)
**Author:** [@rahuldeb](https://gromacs.bioexcel.eu/u/rahuldeb)\ **Replies:** 4\ **Last updated:** [August 31, 2026, 12:11pm UTC](https://gromacs.bioexcel.eu/t/low-gromacs-performance-on-rtx-5090-workstation/13586 "2026-08-31T12:11:55Z")
GROMACS version: 2025.2 GROMACS modification: No Hi everyone, I am seeing unexpectedly low performance on RTX 5090 workstation and would appreciate any suggestions. For the same GROMACS MD simulation (~113k atoms): … --- ## [Subject: How to calculate protein spreading area on a membrane over time using GROMACS and Martini 3](https://gromacs.bioexcel.eu/t/subject-how-to-calculate-protein-spreading-area-on-a-membrane-over-time-using-gromacs-and-martini-3/13688)
**Author:** [@ZXY](https://gromacs.bioexcel.eu/u/ZXY)\ **Replies:** 1\ **Last updated:** [August 31, 2026, 7:38am UTC](https://gromacs.bioexcel.eu/t/subject-how-to-calculate-protein-spreading-area-on-a-membrane-over-time-using-gromacs-and-martini-3/13688 "2026-08-31T07:38:46Z")
Dear GROMACS and Martini users, I am working with a membrane-protein system using the Martini 3 force field and would like to calculate the time-dependent spreading area of a protein (or protein condensate) on the membr… --- ## [Hamiltonian replica exchange error](https://gromacs.bioexcel.eu/t/hamiltonian-replica-exchange-error/13690)
**Author:** [@cbibek](https://gromacs.bioexcel.eu/u/cbibek)\ **Replies:** 1\ **Last updated:** [August 28, 2026, 8:12am UTC](https://gromacs.bioexcel.eu/t/hamiltonian-replica-exchange-error/13690 "2026-08-28T08:12:55Z")
GROMACS version: 2025.2 GROMACS modification: Yes Here post your question I am currently using GROMACS 2025.2 with PLUMED 2.10 and trying to run Hamiltonian replica exchange (HREX). However, I get the following error … --- ## [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… --- ## [How to add salt？](https://gromacs.bioexcel.eu/t/how-to-add-salt/13644)
**Author:** [@ZXY](https://gromacs.bioexcel.eu/u/ZXY)\ **Replies:** 2\ **Last updated:** [August 26, 2026, 1:01pm UTC](https://gromacs.bioexcel.eu/t/how-to-add-salt/13644 "2026-08-26T13:01:03Z")
GROMACS version: GROMACS modification: Yes/No Here post your question I have a question for the community: for the same membrane+protein system in GROMACS with Martini, when using insane to add water and salt at -salt… --- ## [SALADCLOUD Gromacs minimization error Inquiry?](https://gromacs.bioexcel.eu/t/saladcloud-gromacs-minimization-error-inquiry/13684)
**Author:** [@mjsubach](https://gromacs.bioexcel.eu/u/mjsubach)\ **Replies:** 2\ **Last updated:** [August 26, 2026, 6:40am UTC](https://gromacs.bioexcel.eu/t/saladcloud-gromacs-minimization-error-inquiry/13684 "2026-08-26T06:40:15Z")
GROMACS version: GROMACS modification: Yes/No Hello Gromacs Forum I am using SALADCLOUD to run a gromacs simulation using a CHARMM-GUI GENERATED README and associated generated .mdp files. Subsequent to execution, the… --- ## [Results differs in different versions](https://gromacs.bioexcel.eu/t/results-differs-in-different-versions/13683)
**Author:** [@nrdhmal](https://gromacs.bioexcel.eu/u/nrdhmal)\ **Replies:** 2\ **Last updated:** [August 25, 2026, 12:18pm UTC](https://gromacs.bioexcel.eu/t/results-differs-in-different-versions/13683 "2026-08-25T12:18:27Z")
GROMACS version:Gromacs-2023 , Gromacs-2026 GROMACS modification: Yes/No Hello, I am working on a project to study the dielectric constant of the system. I used the gmx current tool to calculate the rotational and tra… --- ## [Tabulated function for 1-4 interactions](https://gromacs.bioexcel.eu/t/tabulated-function-for-1-4-interactions/13681)
**Author:** [@shaunak](https://gromacs.bioexcel.eu/u/shaunak)\ **Replies:** 1\ **Last updated:** [August 25, 2026, 1:56am UTC](https://gromacs.bioexcel.eu/t/tabulated-function-for-1-4-interactions/13681 "2026-08-25T01:56:45Z")
Hi, I was trying to understand how the force is computed for 14 interactions (like coulomb and LJ). I was able to correctly calculate the LJ 14 energy using the standard formula (sum over (c6 / r6 - c12 / r12)) over the… --- ## [Wrapping Inquiry](https://gromacs.bioexcel.eu/t/wrapping-inquiry/13662)
**Author:** [@quantang1903](https://gromacs.bioexcel.eu/u/quantang1903)\ **Replies:** 4\ **Last updated:** [August 24, 2026, 5:27pm UTC](https://gromacs.bioexcel.eu/t/wrapping-inquiry/13662 "2026-08-24T17:27:40Z")
GROMACS version: 2023 GROMACS modification: Yes/No Hello Gromacs users, I have a system which is an aptamer binds to AMP and run for 10us. Since the aptamer is moving inside the PBC a lot, so I tried to wrap it with t… [Next page](https://gromacs.bioexcel.eu/latest.md?page=1)