# \#simulation-setup **URL:** https://gromacs.bioexcel.eu/tag/simulation-setup/49.md [Latest](https://gromacs.bioexcel.eu/latest.md) · [Categories](https://gromacs.bioexcel.eu/categories.md) · [Tags](https://gromacs.bioexcel.eu/tags.md) --- ## [Adding Bond Connection 2'-5' RNA](https://gromacs.bioexcel.eu/t/adding-bond-connection-2-5-rna/13781)
**Author:** [@mandarkulkarni](https://gromacs.bioexcel.eu/u/mandarkulkarni)\ **Replies:** 0\ **Last updated:** [October 21, 2026, 4:17am UTC](https://gromacs.bioexcel.eu/t/adding-bond-connection-2-5-rna/13781 "2026-10-21T04:17:40Z")
GROMACS version: 2026.3 GROMACS modification: Yes / PLUMED Hello, I’m working on a 2’-5’ RNA linkage. I’ve added the relevant RTP and HDB entries, and the force field looks fine. The problem is defining the O2'(i)–P(… --- ## [Chloroform as a solvent in Charmm36 force field](https://gromacs.bioexcel.eu/t/chloroform-as-a-solvent-in-charmm36-force-field/10787)
**Author:** [@mehr](https://gromacs.bioexcel.eu/u/mehr)\ **Replies:** 4\ **Last updated:** [October 18, 2026, 7:17am UTC](https://gromacs.bioexcel.eu/t/chloroform-as-a-solvent-in-charmm36-force-field/10787 "2026-10-18T07:17:48Z")
GROMACS version: 2022.5 GROMACS modification: No I am interested in using chloroform (CHCl3) as a solvent instead of water in the Charmm36 force field. Unfortunately, I couldn’t find any topology for chloroform and sin… --- ## [How create uneven box for all-atom simulation](https://gromacs.bioexcel.eu/t/how-create-uneven-box-for-all-atom-simulation/13771)
**Author:** [@girishparm](https://gromacs.bioexcel.eu/u/girishparm)\ **Replies:** 4\ **Last updated:** [October 15, 2026, 4:45am UTC](https://gromacs.bioexcel.eu/t/how-create-uneven-box-for-all-atom-simulation/13771 "2026-10-15T04:45:58Z")
Gromacs version: 2024.6 Hey everyone, I am working with a protein-membrane system that includes post-translational modifications. I built the whole model using CHARMM-GUI and ran a small minimization using GROMACS as t… --- ## [Position restraints and mdp setup after an AmberTools(ZAFF) -\> ParmEd -\> GROMACS handover](https://gromacs.bioexcel.eu/t/position-restraints-and-mdp-setup-after-an-ambertools-zaff-parmed-gromacs-handover/13768)
**Author:** [@JoyeHye](https://gromacs.bioexcel.eu/u/JoyeHye)\ **Replies:** 0\ **Last updated:** [October 13, 2026, 3:27am UTC](https://gromacs.bioexcel.eu/t/position-restraints-and-mdp-setup-after-an-ambertools-zaff-parmed-gromacs-handover/13768 "2026-10-13T03:27:57Z")
GROMACS version: 2025.4-conda\_forge GROMACS modification: No Hi all, I’m setting up GROMACS MD for a system whose topology was NOT generated by pdb2gmx, but built in AmberTools and converted with ParmEd. I’d apprecia… --- ## [Mdp file differences between CHARMM27 and CHARMM36 parameters](https://gromacs.bioexcel.eu/t/mdp-file-differences-between-charmm27-and-charmm36-parameters/13747)
**Author:** [@ishanipaul](https://gromacs.bioexcel.eu/u/ishanipaul)\ **Replies:** 4\ **Last updated:** [October 7, 2026, 12:01pm UTC](https://gromacs.bioexcel.eu/t/mdp-file-differences-between-charmm27-and-charmm36-parameters/13747 "2026-10-07T12:01:23Z")
GROMACS version: 2024.5 GROMACS modification: No The new version of GROMACS documentation suggests the following modification in the md.mdp file for CHARMM36 forcefield, constraints = h-bonds cutoff-scheme = Verlet … --- ## [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… --- ## [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… --- ## [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… --- ## [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 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… --- ## [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… --- ## [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… --- ## [What if the protein contains mutations and missing residues? ](https://gromacs.bioexcel.eu/t/what-if-the-protein-contains-mutations-and-missing-residues/13492)
**Author:** [@PriZarah](https://gromacs.bioexcel.eu/u/PriZarah)\ **Replies:** 2\ **Last updated:** [June 4, 2026, 7:32am UTC](https://gromacs.bioexcel.eu/t/what-if-the-protein-contains-mutations-and-missing-residues/13492 "2026-06-04T07:32:26Z")
I selected a protein from the protein data bank for my MD simulation study. But the selected protein is not the wild type since it has mutations and missing residues. I was unable to find the wild type as well. So how ca… --- ## [Is there a way to perform simulations with less standard addatives?](https://gromacs.bioexcel.eu/t/is-there-a-way-to-perform-simulations-with-less-standard-addatives/13490)
**Author:** [@Sveakso](https://gromacs.bioexcel.eu/u/Sveakso)\ **Replies:** 3\ **Last updated:** [June 1, 2026, 12:24am UTC](https://gromacs.bioexcel.eu/t/is-there-a-way-to-perform-simulations-with-less-standard-addatives/13490 "2026-06-01T00:24:50Z")
GROMACS version: 2025.4 GROMACS modification: No Hello, Has anyone heard of ways to model non-standard molecules such as TRIS and MOPS buffer components? As in acquire parameters. --- ## [DCLE diffuse into Bulk solution from membrane after 1.8 ns equilbration in HMMM (Charmm-Gui)](https://gromacs.bioexcel.eu/t/dcle-diffuse-into-bulk-solution-from-membrane-after-1-8-ns-equilbration-in-hmmm-charmm-gui/13482)
**Author:** [@swapnil](https://gromacs.bioexcel.eu/u/swapnil)\ **Replies:** 0\ **Last updated:** [May 26, 2026, 5:47am UTC](https://gromacs.bioexcel.eu/t/dcle-diffuse-into-bulk-solution-from-membrane-after-1-8-ns-equilbration-in-hmmm-charmm-gui/13482 "2026-05-26T05:47:03Z")
GROMACS version: 2021.1 GROMACS modification: No Here post your question : I have made a Highly Mobile Membrane-Mimetic Model (HMMM) using CHARMM-GUI which after a equilibration of 1.8 ns, few DCLE diffuse into the bu… --- ## [Simulation box size?](https://gromacs.bioexcel.eu/t/simulation-box-size/13456)
**Author:** [@wurger](https://gromacs.bioexcel.eu/u/wurger)\ **Replies:** 7\ **Last updated:** [May 19, 2026, 2:44pm UTC](https://gromacs.bioexcel.eu/t/simulation-box-size/13456 "2026-05-19T14:44:47Z")
GROMACS version: gromacs/2024.2 GROMACS modification: No Beginner MD user here with a beginner question. I’m setting up a simulation of a globular soluble protein with a longest axis of ~5.5 nm. I’ve tried generating … --- ## [COM motion removal during NVT simulation with electric field](https://gromacs.bioexcel.eu/t/com-motion-removal-during-nvt-simulation-with-electric-field/13447)
**Author:** [@Afi](https://gromacs.bioexcel.eu/u/Afi)\ **Replies:** 5\ **Last updated:** [May 19, 2026, 6:18am UTC](https://gromacs.bioexcel.eu/t/com-motion-removal-during-nvt-simulation-with-electric-field/13447 "2026-05-19T06:18:22Z")
Hi, I am studying the motion of a positively charged protein in the presence of electric field at 300 K. I have observed a conflict between maintaining the physical drift of the protein under the influence of electric f… --- ## [LINCS Error in production run](https://gromacs.bioexcel.eu/t/lincs-error-in-production-run/10434)
**Author:** [@athiras](https://gromacs.bioexcel.eu/u/athiras)\ **Replies:** 2\ **Last updated:** [May 1, 2026, 10:45am UTC](https://gromacs.bioexcel.eu/t/lincs-error-in-production-run/10434 "2026-05-01T10:45:24Z")
GROMACS version: 2021.1 GROMACS modification: Yes/No Here post your question I am currently running a 1 ns production molecular dynamics (MD) simulation with restraints, but I’m encountering persistent LINCS warnings … --- ## [PBC/trajectory reconstruction problem for discontinuous multi-chain RNA fragment](https://gromacs.bioexcel.eu/t/pbc-trajectory-reconstruction-problem-for-discontinuous-multi-chain-rna-fragment/13424)
**Author:** [@hwang](https://gromacs.bioexcel.eu/u/hwang)\ **Replies:** 0\ **Last updated:** [April 28, 2026, 8:53pm UTC](https://gromacs.bioexcel.eu/t/pbc-trajectory-reconstruction-problem-for-discontinuous-multi-chain-rna-fragment/13424 "2026-04-28T20:53:42Z")
Hi, I have a small RNA construct excised from a much larger RNA/protein complex. For confidentiality reasons I cannot share the exact biological identity of the construct, but the relevant technical details are: The s… --- ## [One system not plateauing in NPT before SMD comparison across multiple complexes](https://gromacs.bioexcel.eu/t/one-system-not-plateauing-in-npt-before-smd-comparison-across-multiple-complexes/13419)
**Author:** [@rachana](https://gromacs.bioexcel.eu/u/rachana)\ **Replies:** 0\ **Last updated:** [April 28, 2026, 3:19am UTC](https://gromacs.bioexcel.eu/t/one-system-not-plateauing-in-npt-before-smd-comparison-across-multiple-complexes/13419 "2026-04-28T03:19:13Z")
GROMACS version: gromacs/2025.3-openmpi-5.0.8-single-rocky8 GROMACS modification: Yes/No Here post your question I am comparing 4 TCR–pMHC complexes using constant-velocity SMD and want to compare rupture force, peak … --- ## [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… --- ## [GROMACS SMD for TCR–pMHC: should TCR be pull group 1 or 2](https://gromacs.bioexcel.eu/t/gromacs-smd-for-tcr-pmhc-should-tcr-be-pull-group-1-or-2/13414)
**Author:** [@rachana](https://gromacs.bioexcel.eu/u/rachana)\ **Replies:** 0\ **Last updated:** [April 25, 2026, 10:04pm UTC](https://gromacs.bioexcel.eu/t/gromacs-smd-for-tcr-pmhc-should-tcr-be-pull-group-1-or-2/13414 "2026-04-25T22:04:25Z")
GROMACS version: GROMACS modification: Yes/No Here post your question I am setting up constant-velocity SMD for a TCR–pMHC system. The C-terminal Cα of the MHC α-chain is position-restrained as the anchor, and the pul… --- ## [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… --- ## [Simulating a protein or DNA with multiple ligands](https://gromacs.bioexcel.eu/t/simulating-a-protein-or-dna-with-multiple-ligands/13339)
**Author:** [@Trideep](https://gromacs.bioexcel.eu/u/Trideep)\ **Replies:** 2\ **Last updated:** [April 7, 2026, 3:47pm UTC](https://gromacs.bioexcel.eu/t/simulating-a-protein-or-dna-with-multiple-ligands/13339 "2026-04-07T15:47:12Z")
GROMACS version:2020.6 GROMACS modification: Yes/No Here post your question I am a beginner with gromacs. I have just started to learn some basics. Can anybody help me regarding how to set up a system for performing a… --- ## [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… --- ## [Virtual site creation](https://gromacs.bioexcel.eu/t/virtual-site-creation/13363)
**Author:** [@mjm91](https://gromacs.bioexcel.eu/u/mjm91)\ **Replies:** 0\ **Last updated:** [April 5, 2026, 9:27am UTC](https://gromacs.bioexcel.eu/t/virtual-site-creation/13363 "2026-04-05T09:27:33Z")
Dear gromacs users, I am working with a simulation of C60 fullerenes in water. One problem I faced is that during solvation step and subsequent steps of the MD, water molecules enter the fullerene cavity. Also I don’t w… --- ## [Multicomponent system](https://gromacs.bioexcel.eu/t/multicomponent-system/13327)
**Author:** [@Maayan](https://gromacs.bioexcel.eu/u/Maayan)\ **Replies:** 1\ **Last updated:** [April 1, 2026, 5:21pm UTC](https://gromacs.bioexcel.eu/t/multicomponent-system/13327 "2026-04-01T17:21:53Z")
Hello, I am a master’s student new to MD simulations, and I have a few questions about building a multicomponent membrane system. Background: I have an existing POPC bilayer (100 lipids/leaflet) built with CHARMM-GUI,… --- ## [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… --- ## [Problem using Position restraints for multiple groups](https://gromacs.bioexcel.eu/t/problem-using-position-restraints-for-multiple-groups/13340)
**Author:** [@fredpontes20](https://gromacs.bioexcel.eu/u/fredpontes20)\ **Replies:** 2\ **Last updated:** [March 30, 2026, 10:49am UTC](https://gromacs.bioexcel.eu/t/problem-using-position-restraints-for-multiple-groups/13340 "2026-03-30T10:49:29Z")
GROMACS version: 2023.2 GROMACS modification: No I have a membrane-protein system and during the pre-equilibration I’m applying different values of positional restraints for lipids (6 different species) and the protein… [Next page](https://gromacs.bioexcel.eu/tag/simulation-setup/49.md?match_all_tags=true&page=1&tags%5B%5D=simulation-setup)