# User discussions **URL:** https://gromacs.bioexcel.eu/c/gromacs-user-forum/5.md?page=3 [Latest](https://gromacs.bioexcel.eu/latest.md) · [Categories](https://gromacs.bioexcel.eu/categories.md) · [Tags](https://gromacs.bioexcel.eu/tags.md) **Page:** 4 --- ## [RMSD for Protein-Ligand complex](https://gromacs.bioexcel.eu/t/rmsd-for-protein-ligand-complex/9974)
**Author:** [@rhb106](https://gromacs.bioexcel.eu/u/rhb106)\ **Replies:** 2\ **Last updated:** [July 13, 2026, 4:12am UTC](https://gromacs.bioexcel.eu/t/rmsd-for-protein-ligand-complex/9974 "2026-07-13T04:12:21Z")
Hello,I’m new in GROMACS. I’m facing a problem with RMSD calculation for protein-ligand complex.After running the code for RMSD,what should I choose for RMSD calculation if I want to create graph like the attached pictur… --- ## [Trajectory preprocessing in peptide self-assembly simulations](https://gromacs.bioexcel.eu/t/trajectory-preprocessing-in-peptide-self-assembly-simulations/13596)
**Author:** [@Deniz](https://gromacs.bioexcel.eu/u/Deniz)\ **Replies:** 0\ **Last updated:** [July 12, 2026, 6:12pm UTC](https://gromacs.bioexcel.eu/t/trajectory-preprocessing-in-peptide-self-assembly-simulations/13596 "2026-07-12T18:12:17Z")
GROMACS version: GROMACS modification: No Dear all, I performed molecular dynamics simulations of peptide self-assembly using GROMACS. My system consists of 150 antimicrobial peptides (13 amino acids each) simulated i… --- ## [gmx\_MMPBSA for big molecule](https://gromacs.bioexcel.eu/t/gmx-mmpbsa-for-big-molecule/13589)
**Author:** [@Diahdd96](https://gromacs.bioexcel.eu/u/Diahdd96)\ **Replies:** 1\ **Last updated:** [July 10, 2026, 6:30pm UTC](https://gromacs.bioexcel.eu/t/gmx-mmpbsa-for-big-molecule/13589 "2026-07-10T18:30:38Z")
GROMACS version: 2018 I tried several times on fixing error of gmx\_MMPBSA for protein 3VSL (s.aureus) with claude.ai but it seemed endless. the error look like this : \[INFO \] parmchk2 found! Using /home/diah/minicond… --- ## [PBC correction for ionisable lipid–lipid bilayer system (GROMACS 2025.4)](https://gromacs.bioexcel.eu/t/pbc-correction-for-ionisable-lipid-lipid-bilayer-system-gromacs-2025-4/13592)
**Author:** [@Drashti](https://gromacs.bioexcel.eu/u/Drashti)\ **Replies:** 0\ **Last updated:** [July 10, 2026, 12:02pm UTC](https://gromacs.bioexcel.eu/t/pbc-correction-for-ionisable-lipid-lipid-bilayer-system-gromacs-2025-4/13592 "2026-07-10T12:02:06Z")
GROMACS version:2025.4 GROMACS modification: No Dear GROMACS users, I am working with ionisable lipid–membrane lipid bilayer system simulated for 500 ns. I would like to apply PBC corrections to obtain a proper trajec… --- ## [GROMACS Courtesy](https://gromacs.bioexcel.eu/t/gromacs-courtesy/13588)
**Author:** [@Abhinandan](https://gromacs.bioexcel.eu/u/Abhinandan)\ **Replies:** 0\ **Last updated:** [July 10, 2026, 3:31am UTC](https://gromacs.bioexcel.eu/t/gromacs-courtesy/13588 "2026-07-10T03:31:37Z")
To the Concerned Respected Sir / Madam Good Morning Hope everyone is in good health This e-mail is to share, write and inform that i could manage to complete the Doctor of Philosophy (PhD) from the University of Calc… --- ## [TIP4P/Ice .itp File](https://gromacs.bioexcel.eu/t/tip4p-ice-itp-file/13587)
**Author:** [@MDinda](https://gromacs.bioexcel.eu/u/MDinda)\ **Replies:** 0\ **Last updated:** [July 9, 2026, 7:36pm UTC](https://gromacs.bioexcel.eu/t/tip4p-ice-itp-file/13587 "2026-07-09T19:36:27Z")
GROMACS version: 2021.4 I would like to study an ice–water system using the TIP4P/Ice model. Could you please confirm whether the same .itp file is used for both TIP4P/Ice water and ice systems? --- ## [gmx\_MMPBSA error in Steered Molecular dynamics simulation trajectory](https://gromacs.bioexcel.eu/t/gmx-mmpbsa-error-in-steered-molecular-dynamics-simulation-trajectory/13544)
**Author:** [@shrmi\_m](https://gromacs.bioexcel.eu/u/shrmi_m)\ **Replies:** 1\ **Last updated:** [July 9, 2026, 9:03am UTC](https://gromacs.bioexcel.eu/t/gmx-mmpbsa-error-in-steered-molecular-dynamics-simulation-trajectory/13544 "2026-07-09T09:03:57Z")
GROMACS version: 2024.1 GROMACS modification: No Hi, hope you all are doing well. I faced an error while performing gmx\_mmpbsa for my smd trajectory file. here is the problem: it says that it can not find the atom no.… --- ## [G\_mmpbsa for the gromacs 2025 versions](https://gromacs.bioexcel.eu/t/g-mmpbsa-for-the-gromacs-2025-versions/13580)
**Author:** [@jhfernandez](https://gromacs.bioexcel.eu/u/jhfernandez)\ **Replies:** 1\ **Last updated:** [July 9, 2026, 8:57am UTC](https://gromacs.bioexcel.eu/t/g-mmpbsa-for-the-gromacs-2025-versions/13580 "2026-07-09T08:57:38Z")
GROMACS version: 2025.x GROMACS modification: Yes/No Good morning (afternoon, or evening), everyone. We are attempting to revive an old project that relied heavily on the now-defunct “g\_mmpbsa” tool within the GROMACS… --- ## [Atoms not completely removed by convert-tpr](https://gromacs.bioexcel.eu/t/atoms-not-completely-removed-by-convert-tpr/13526)
**Author:** [@Erik](https://gromacs.bioexcel.eu/u/Erik)\ **Replies:** 3\ **Last updated:** [July 8, 2026, 8:04am UTC](https://gromacs.bioexcel.eu/t/atoms-not-completely-removed-by-convert-tpr/13526 "2026-07-08T08:04:18Z")
GROMACS version: 2025.1 GROMACS modification: No I’m trying to perform analysis using only part of a molecule (Removing the ends of a nucleic acid strand). Because of how my downstream analysis pipeline works, I determ… --- ## [PBC wrapping for Protein-Ligand-Surface system](https://gromacs.bioexcel.eu/t/pbc-wrapping-for-protein-ligand-surface-system/13581)
**Author:** [@Gvantsa](https://gromacs.bioexcel.eu/u/Gvantsa)\ **Replies:** 0\ **Last updated:** [July 7, 2026, 4:45pm UTC](https://gromacs.bioexcel.eu/t/pbc-wrapping-for-protein-ligand-surface-system/13581 "2026-07-07T16:45:04Z")
GROMACS version: 2025.2 GROMACS modification: No Hi everyone, I am struggling with PBC wrapping artifacts in a system involving a protein-ligand (GTP) complex interacting with a Laponite clay surface\*\*(infinite sheet)… --- ## [Use of refcoordscaling in CHARMM and MARTINI](https://gromacs.bioexcel.eu/t/use-of-refcoordscaling-in-charmm-and-martini/13578)
**Author:** [@amarkrishna10](https://gromacs.bioexcel.eu/u/amarkrishna10)\ **Replies:** 0\ **Last updated:** [July 7, 2026, 8:58am UTC](https://gromacs.bioexcel.eu/t/use-of-refcoordscaling-in-charmm-and-martini/13578 "2026-07-07T08:58:02Z")
I notice that the refcoordscaling option in the mdp files from CHARMM-GUI have the following values: com, in CHARMM all, in MARTINI. I understand the basic logic behind the use of this option, but I was wondering the … --- ## [Workstation options](https://gromacs.bioexcel.eu/t/workstation-options/13179)
**Author:** [@farah1](https://gromacs.bioexcel.eu/u/farah1)\ **Replies:** 2\ **Last updated:** [July 7, 2026, 6:53am UTC](https://gromacs.bioexcel.eu/t/workstation-options/13179 "2026-07-07T06:53:00Z")
Hi everyone, I’m planning to buy a workstation mainly for GROMACS simulations, but I’m confused between two options within my budget: Option A: RTX 5080 + 64 GB RAM Option B: RTX 5090 + 32 GB RAM From a GROMACS perfo… --- ## [Can CGenFF-generated partial charges differ significantly from QM-derived CHELPG (ESP) charges?](https://gromacs.bioexcel.eu/t/can-cgenff-generated-partial-charges-differ-significantly-from-qm-derived-chelpg-esp-charges/13566)
**Author:** [@Somdatta](https://gromacs.bioexcel.eu/u/Somdatta)\ **Replies:** 2\ **Last updated:** [July 5, 2026, 9:59am UTC](https://gromacs.bioexcel.eu/t/can-cgenff-generated-partial-charges-differ-significantly-from-qm-derived-chelpg-esp-charges/13566 "2026-07-05T09:59:39Z")
Hello everyone, I am parameterizing a protonated molecule for molecular dynamics simulations using the CHARMM36/CGenFF force field. My workflow was as follows: I used the MP2/cc-pVDZ optimized geometry of the molecul… --- ## [RMSD analysis of the Protein-Ligand simulation](https://gromacs.bioexcel.eu/t/rmsd-analysis-of-the-protein-ligand-simulation/13574)
**Author:** [@kalsiAMAN](https://gromacs.bioexcel.eu/u/kalsiAMAN)\ **Replies:** 0\ **Last updated:** [July 5, 2026, 7:14am UTC](https://gromacs.bioexcel.eu/t/rmsd-analysis-of-the-protein-ligand-simulation/13574 "2026-07-05T07:14:25Z")
GROMACS version: 2023.2 GROMACS modification: Yes/No Here post your question Hey , I hope everythings fine. I had query regarding the Index file preparation using gromacs command gmx make\_ndx. after successfull runnin… --- ## [How many nanoseconds do I need to capture potential unbinding events for protein-protein interaction](https://gromacs.bioexcel.eu/t/how-many-nanoseconds-do-i-need-to-capture-potential-unbinding-events-for-protein-protein-interaction/13572)
**Author:** [@Kael](https://gromacs.bioexcel.eu/u/Kael)\ **Replies:** 1\ **Last updated:** [July 4, 2026, 3:10pm UTC](https://gromacs.bioexcel.eu/t/how-many-nanoseconds-do-i-need-to-capture-potential-unbinding-events-for-protein-protein-interaction/13572 "2026-07-04T15:10:40Z")
GROMACS version: 2026.1 GROMACS modification: No Hi! I’m currently performing MD analysis of receptor-cytokine interaction (ppi) within 200 nanoseconds. I’m testing single-point mutation on cytokines, and I want to ca… --- ## [How to deal with Zn ion in Zinc finger protein](https://gromacs.bioexcel.eu/t/how-to-deal-with-zn-ion-in-zinc-finger-protein/13557)
**Author:** [@JoyeHye](https://gromacs.bioexcel.eu/u/JoyeHye)\ **Replies:** 3\ **Last updated:** [July 3, 2026, 10:03am UTC](https://gromacs.bioexcel.eu/t/how-to-deal-with-zn-ion-in-zinc-finger-protein/13557 "2026-07-03T10:03:29Z")
GROMACS version: 2025.4-conda\_forge GROMACS modification: No I am currently conducting simulations on the binding mechanism between a zinc finger protein and a segment of DNA sequence. This zinc finger protein contains… --- ## [GROMACS 2026.2 duplicate type-9 dihedral errors with CHARMM36-feb2026 and CGenFF 5.0](https://gromacs.bioexcel.eu/t/gromacs-2026-2-duplicate-type-9-dihedral-errors-with-charmm36-feb2026-and-cgenff-5-0/13570)
**Author:** [@myneni](https://gromacs.bioexcel.eu/u/myneni)\ **Replies:** 1\ **Last updated:** [July 3, 2026, 1:38am UTC](https://gromacs.bioexcel.eu/t/gromacs-2026-2-duplicate-type-9-dihedral-errors-with-charmm36-feb2026-and-cgenff-5-0/13570 "2026-07-03T01:38:50Z")
Hi everyone, I am performing a protein–ligand MD simulation using GROMACS 2026.2 CHARMM36-feb2026 CGenFF 5.0 Ligand topology was generated using the latest cgenff\_charmm2gmx.py (March 2025 David Moody version). Co… --- ## [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… --- ## [How to generate a MOL2 ligand file with the correct docking pose, full hydrogens, and physiological](https://gromacs.bioexcel.eu/t/how-to-generate-a-mol2-ligand-file-with-the-correct-docking-pose-full-hydrogens-and-physiological/13548)
**Author:** [@lhtrunggnhan](https://gromacs.bioexcel.eu/u/lhtrunggnhan)\ **Replies:** 1\ **Last updated:** [July 1, 2026, 10:26am UTC](https://gromacs.bioexcel.eu/t/how-to-generate-a-mol2-ligand-file-with-the-correct-docking-pose-full-hydrogens-and-physiological/13548 "2026-07-01T10:26:27Z")
GROMACS version: 2026.2 GROMACS modification: No Hello everyone, I am currently preparing a molecular dynamics simulation for a protein–ligand complex. The ligand pose was obtained from molecular docking using AutoDoc… --- ## [Efficient Workflow for Multiple Modified Residues](https://gromacs.bioexcel.eu/t/efficient-workflow-for-multiple-modified-residues/13565)
**Author:** [@marusya](https://gromacs.bioexcel.eu/u/marusya)\ **Replies:** 2\ **Last updated:** [July 1, 2026, 10:17am UTC](https://gromacs.bioexcel.eu/t/efficient-workflow-for-multiple-modified-residues/13565 "2026-07-01T10:17:01Z")
GROMACS version: 2022.4 GROMACS modification: No Hi all, I need to perform molecular dynamics simulations of multiple ligands that are covalently attached to cysteine residues. Is there an automated way to generate th… --- ## [Ligand jumping around during GROMACS MD simulation after CHARMM-GUI setup – PBC issue or system prep](https://gromacs.bioexcel.eu/t/ligand-jumping-around-during-gromacs-md-simulation-after-charmm-gui-setup-pbc-issue-or-system-prep/13561)
**Author:** [@lhtrunggnhan](https://gromacs.bioexcel.eu/u/lhtrunggnhan)\ **Replies:** 1\ **Last updated:** [June 26, 2026, 10:46pm UTC](https://gromacs.bioexcel.eu/t/ligand-jumping-around-during-gromacs-md-simulation-after-charmm-gui-setup-pbc-issue-or-system-prep/13561 "2026-06-26T22:46:35Z")
GROMACS version: 2026.2 GROMACS modification: No Hi everyone, I’m running my first molecular dynamics simulation of a usnic acid derivative and would really appreciate some advice. I started from the best docking pos… --- ## [Gromacs 2025.4 + Plumed 2.10 Installation issue](https://gromacs.bioexcel.eu/t/gromacs-2025-4-plumed-2-10-installation-issue/13560)
**Author:** [@mandarkulkarni](https://gromacs.bioexcel.eu/u/mandarkulkarni)\ **Replies:** 0\ **Last updated:** [June 26, 2026, 9:12am UTC](https://gromacs.bioexcel.eu/t/gromacs-2025-4-plumed-2-10-installation-issue/13560 "2026-06-26T09:12:52Z")
GROMACS version: 2025.4 GROMACS modification: Yes Here post your question Hi, I am trying to install Gromacs 2025.4 + PLUMED 2.10 on server with H100 GPUS. nvcc version: 12.3 cmake version: 4.3.4 nvidia driver: 59… --- ## [Trying to perturb a torsion with multiple terms](https://gromacs.bioexcel.eu/t/trying-to-perturb-a-torsion-with-multiple-terms/13558)
**Author:** [@alfredo](https://gromacs.bioexcel.eu/u/alfredo)\ **Replies:** 1\ **Last updated:** [June 25, 2026, 6:40pm UTC](https://gromacs.bioexcel.eu/t/trying-to-perturb-a-torsion-with-multiple-terms/13558 "2026-06-25T18:40:55Z")
GROMACS version:gromacs-2025.2 GROMACS modification: No Hi, I would like to run a FEP simulation of a peptide for which I want to annihilate a terminal amino acid. I am using CHARMM force field and several torsions tha… --- ## [Protein small molecule simulation](https://gromacs.bioexcel.eu/t/protein-small-molecule-simulation/13469)
**Author:** [@Trideep](https://gromacs.bioexcel.eu/u/Trideep)\ **Replies:** 3\ **Last updated:** [June 25, 2026, 5:15am UTC](https://gromacs.bioexcel.eu/t/protein-small-molecule-simulation/13469 "2026-06-25T05:15:31Z")
GROMACS version:2020.6 GROMACS modification: Yes/No Here post your question I want to simulate an IDP protein with a small molecule. I want to add 10 copies of the same molecule into the simulation box randomly and lo… --- ## [Temperature coupling](https://gromacs.bioexcel.eu/t/temperature-coupling/13547)
**Author:** [@slaa1999](https://gromacs.bioexcel.eu/u/slaa1999)\ **Replies:** 3\ **Last updated:** [June 24, 2026, 4:27pm UTC](https://gromacs.bioexcel.eu/t/temperature-coupling/13547 "2026-06-24T16:27:17Z")
GROMACS version:2020.7 GROMACS modification: Yes/No Hello All, Excuse my novice experience in GROMACS MD simulation. What is the approach in setting up proper control of temperature coupling. I have system with a met… --- ## [Standard publishable preprocessing of AlphaFold3 complex structures for GROMACS MD simulations](https://gromacs.bioexcel.eu/t/standard-publishable-preprocessing-of-alphafold3-complex-structures-for-gromacs-md-simulations/13553)
**Author:** [@JoyeHye](https://gromacs.bioexcel.eu/u/JoyeHye)\ **Replies:** 0\ **Last updated:** [June 24, 2026, 2:30pm UTC](https://gromacs.bioexcel.eu/t/standard-publishable-preprocessing-of-alphafold3-complex-structures-for-gromacs-md-simulations/13553 "2026-06-24T14:30:58Z")
GROMACS version: 2025.4-conda\_forge GROMACS modification: No Hello, I am wondering what are standard publishable preprocessing workflows for AlphaFold3-predicted complex structures to prepare them for GROMACS MD simula… --- ## [Gromacs warning when calculating RMSD: excessively large distances exist or the system is exploding](https://gromacs.bioexcel.eu/t/gromacs-warning-when-calculating-rmsd-excessively-large-distances-exist-or-the-system-is-exploding/13549)
**Author:** [@EduardoGarcia](https://gromacs.bioexcel.eu/u/EduardoGarcia)\ **Replies:** 1\ **Last updated:** [June 24, 2026, 6:36am UTC](https://gromacs.bioexcel.eu/t/gromacs-warning-when-calculating-rmsd-excessively-large-distances-exist-or-the-system-is-exploding/13549 "2026-06-24T06:36:10Z")
GROMACS version: 2023 GROMACS modification: No Hello everyone, I hope you can help me solve a problem Gromacs generates when performing a molecular dynamics analysis: inconsistent shifts are observed in the periodic… --- ## [Fatal Error: no domain decomposition for rank 4, min cell size 1.776 nm](https://gromacs.bioexcel.eu/t/fatal-error-no-domain-decomposition-for-rank-4-min-cell-size-1-776-nm/13550)
**Author:** [@sgarey](https://gromacs.bioexcel.eu/u/sgarey)\ **Replies:** 1\ **Last updated:** [June 24, 2026, 6:34am UTC](https://gromacs.bioexcel.eu/t/fatal-error-no-domain-decomposition-for-rank-4-min-cell-size-1-776-nm/13550 "2026-06-24T06:34:12Z")
GROMACS version:2022.4 GROMACS modification: Yes/No I am trying to run free energy calculation for the 20 standard amino acids. My simulations ran fine for smaller amino acids like glycine, but I’m having this issue wi… --- ## [GROMACS pdb2gmx Warning: Missing Atoms (H and O) in AlphaFold3-Derived TCR–pMHC Structure](https://gromacs.bioexcel.eu/t/gromacs-pdb2gmx-warning-missing-atoms-h-and-o-in-alphafold3-derived-tcr-pmhc-structure/13234)
**Author:** [@rachana](https://gromacs.bioexcel.eu/u/rachana)\ **Replies:** 1\ **Last updated:** [June 24, 2026, 2:48am UTC](https://gromacs.bioexcel.eu/t/gromacs-pdb2gmx-warning-missing-atoms-h-and-o-in-alphafold3-derived-tcr-pmhc-structure/13234 "2026-06-24T02:48:19Z")
GROMACS version: gromacs/2025.3-openmpi-5.0.8-single-rocky8 GROMACS modification: Yes/No Here post your question I am new to using GROMACS as I mostly deal with omics data I am using this for my TCR-pMHC structural mo… --- ## [TIP4P/2005 water model](https://gromacs.bioexcel.eu/t/tip4p-2005-water-model/3666)
**Author:** [@Lida](https://gromacs.bioexcel.eu/u/Lida)\ **Replies:** 2\ **Last updated:** [June 22, 2026, 7:24am UTC](https://gromacs.bioexcel.eu/t/tip4p-2005-water-model/3666 "2026-06-22T07:24:15Z")
GROMACS version: 2020 GROMACS modification: Yes/No Hello everyone, I would like to use tip4p/2005 water model in my simulation. However, I couldn’t find any of the force fields that are compatible with this water mode… [Previous page](https://gromacs.bioexcel.eu/c/gromacs-user-forum/5.md?page=2) [Next page](https://gromacs.bioexcel.eu/c/gromacs-user-forum/5.md?page=4)