# \#grompp **URL:** https://gromacs.bioexcel.eu/tag/grompp/7.md [Latest](https://gromacs.bioexcel.eu/latest.md) · [Categories](https://gromacs.bioexcel.eu/categories.md) · [Tags](https://gromacs.bioexcel.eu/tags.md) --- ## [C-rescale barostat and simulated annealing](https://gromacs.bioexcel.eu/t/c-rescale-barostat-and-simulated-annealing/13652)
**Author:** [@Marius](https://gromacs.bioexcel.eu/u/Marius)\ **Replies:** 4\ **Last updated:** [August 6, 2026, 2:48pm UTC](https://gromacs.bioexcel.eu/t/c-rescale-barostat-and-simulated-annealing/13652 "2026-08-06T14:48:24Z")
GROMACS version: 2025.4 / 2021 GROMACS modification: 2025.4 (No) / 2021 (Yes) Hi, I recently stumbled across an issue running grompp for a simulation using simulated annealing. For temperature coupling I am using the … --- ## [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… --- ## [Performance regression in 2025.4: suboptimal CUDA NBNxM kernel selection vs 2024.2](https://gromacs.bioexcel.eu/t/performance-regression-in-2025-4-suboptimal-cuda-nbnxm-kernel-selection-vs-2024-2/13112)
**Author:** [@alexmas](https://gromacs.bioexcel.eu/u/alexmas)\ **Replies:** 7\ **Last updated:** [February 12, 2026, 7:54am UTC](https://gromacs.bioexcel.eu/t/performance-regression-in-2025-4-suboptimal-cuda-nbnxm-kernel-selection-vs-2024-2/13112 "2026-02-12T07:54:46Z")
GROMACS version: 2024.2 + 2025.4 GROMACS modification: No I am observing a significant performance regression in GROMACS 2025.4 compared to 2024.2 for a realistic protein-in-water system on a single GPU. The regression… --- ## [no default bond types, angle types or dihedral types](https://gromacs.bioexcel.eu/t/no-default-bond-types-angle-types-or-dihedral-types/13151)
**Author:** [@MckMarco](https://gromacs.bioexcel.eu/u/MckMarco)\ **Replies:** 1\ **Last updated:** [February 4, 2026, 10:36am UTC](https://gromacs.bioexcel.eu/t/no-default-bond-types-angle-types-or-dihedral-types/13151 "2026-02-04T10:36:46Z")
I am trying to do protein-ligand complex md and am receiving the errors above. I have generated the ligand .itp files in the charmm-gui, I have the charmm.itp file that has the defaults in, but when i include both those … --- ## [Simulating a Reverse Transcriptase complex with RNA, DNA](https://gromacs.bioexcel.eu/t/simulating-a-reverse-transcriptase-complex-with-rna-dna/12984)
**Author:** [@bhavya\_28](https://gromacs.bioexcel.eu/u/bhavya_28)\ **Replies:** 1\ **Last updated:** [December 1, 2025, 4:58am UTC](https://gromacs.bioexcel.eu/t/simulating-a-reverse-transcriptase-complex-with-rna-dna/12984 "2025-12-01T04:58:50Z")
Hi, I have been trying to simulate a reverse transcriptase (PDB 6AR1) that is in complex with RNA, DNA, DTPs, MG, SO4. Gromacs cribs because it cannot recognise if the Mg, DTP, SO4 is in the same chain as the protein. An… --- ## [Pdb2gmx not recognizing water block](https://gromacs.bioexcel.eu/t/pdb2gmx-not-recognizing-water-block/12865)
**Author:** [@krb0073](https://gromacs.bioexcel.eu/u/krb0073)\ **Replies:** 1\ **Last updated:** [November 11, 2025, 11:37am UTC](https://gromacs.bioexcel.eu/t/pdb2gmx-not-recognizing-water-block/12865 "2025-11-11T11:37:13Z")
GROMACS version: 2022.5-Debian\_2022.5\_2 GROMACS modification: No Hello all, I have been trying to create a system using pdb2gmx to generate the topology of a membrane system. pdb2gmx runs to completion, but the wa… --- ## [Assertion failed for buckingham interacting solid](https://gromacs.bioexcel.eu/t/assertion-failed-for-buckingham-interacting-solid/12843)
**Author:** [@manuelperezesc](https://gromacs.bioexcel.eu/u/manuelperezesc)\ **Replies:** 1\ **Last updated:** [October 28, 2025, 1:38pm UTC](https://gromacs.bioexcel.eu/t/assertion-failed-for-buckingham-interacting-solid/12843 "2025-10-28T13:38:29Z")
GROMACS version: 2024.5 GROMACS modification: No I am very new to Gromacs and I would like to run dynamics for a solid using a Buckingham potential but I guess I am missing something in the topology definition of my sy… --- ## [How to setup protein-ligand simulation using CHARMM-GUI for ligand preparation](https://gromacs.bioexcel.eu/t/how-to-setup-protein-ligand-simulation-using-charmm-gui-for-ligand-preparation/12721)
**Author:** [@Caterpillar](https://gromacs.bioexcel.eu/u/Caterpillar)\ **Replies:** 9\ **Last updated:** [October 26, 2025, 5:51pm UTC](https://gromacs.bioexcel.eu/t/how-to-setup-protein-ligand-simulation-using-charmm-gui-for-ligand-preparation/12721 "2025-10-26T17:51:00Z")
GROMACS version: 2025.3 GROMACS modification: No Goal: I would like help getting the protein-ligand tutorial working with GROMACS 2025.3 and using CHARMM-GUI to produce the ligand parameters. I am stuck at the step of… --- ## [How to simulate a cyclic protein with AMBER99SB ff?](https://gromacs.bioexcel.eu/t/how-to-simulate-a-cyclic-protein-with-amber99sb-ff/12742)
**Author:** [@bee9](https://gromacs.bioexcel.eu/u/bee9)\ **Replies:** 1\ **Last updated:** [October 9, 2025, 8:51am UTC](https://gromacs.bioexcel.eu/t/how-to-simulate-a-cyclic-protein-with-amber99sb-ff/12742 "2025-10-09T08:51:05Z")
Hello, I am trying to simulate a protein which I cyclized using Chimera. I have referred to the articles https://pubs.acs.org/doi/10.1021/acs.jpcb.4c00157 and followed this tutorial ( CP\_tutorial/Tutorials at main · ysl-… --- ## [Problems with generating self contained topology file (necessary for partial tempering with plumed)](https://gromacs.bioexcel.eu/t/problems-with-generating-self-contained-topology-file-necessary-for-partial-tempering-with-plumed/12708)
**Author:** [@Blue](https://gromacs.bioexcel.eu/u/Blue)\ **Replies:** 1\ **Last updated:** [September 29, 2025, 1:16pm UTC](https://gromacs.bioexcel.eu/t/problems-with-generating-self-contained-topology-file-necessary-for-partial-tempering-with-plumed/12708 "2025-09-29T13:16:40Z")
GROMACS version: 2025.3 GROMACS modification: Yes (patched with PLUMED 2.9.4) Here post your question Hello, it’s me again with another question. I want to set up HREX MD simulations with plumed. For that, I need a s… --- ## [RMSD graph after protein protein md simulation](https://gromacs.bioexcel.eu/t/rmsd-graph-after-protein-protein-md-simulation/12615)
**Author:** [@Satarups](https://gromacs.bioexcel.eu/u/Satarups)\ **Replies:** 4\ **Last updated:** [September 8, 2025, 3:23pm UTC](https://gromacs.bioexcel.eu/t/rmsd-graph-after-protein-protein-md-simulation/12615 "2025-09-08T15:23:39Z")
GROMACS version: GROMACS modification: Yes/No Here post your question I did protein-protein MD simulation and did equilibration for 500ns. First for 200ns then extended till 500ns. After pbc mol, centering,in RMSD i s… --- ## [Molecule type 'Protein\_chain\_A' contains no atoms](https://gromacs.bioexcel.eu/t/molecule-type-protein-chain-a-contains-no-atoms/12179)
**Author:** [@Ntieche1](https://gromacs.bioexcel.eu/u/Ntieche1)\ **Replies:** 1\ **Last updated:** [June 2, 2025, 6:50am UTC](https://gromacs.bioexcel.eu/t/molecule-type-protein-chain-a-contains-no-atoms/12179 "2025-06-02T06:50:44Z")
GROMACS version: GROMACS modification: Yes/No Here post your question I am a newsly user trying to perform molecular dynamics with the basic gramocs tutorials without any modifications and I have this error . I nee… --- ## [Need help minimising a backmapped system (I used backward method)](https://gromacs.bioexcel.eu/t/need-help-minimising-a-backmapped-system-i-used-backward-method/12066)
**Author:** [@Oh\_men\_its\_gromacs](https://gromacs.bioexcel.eu/u/Oh_men_its_gromacs)\ **Replies:** 0\ **Last updated:** [May 12, 2025, 1:45pm UTC](https://gromacs.bioexcel.eu/t/need-help-minimising-a-backmapped-system-i-used-backward-method/12066 "2025-05-12T13:45:31Z")
GROMACS version:2023.3 GROMACS modification: Yes/No Hi everyone, I’m using backward.py and/or the initram script for backmapping. During the energy minimization step, I get errors when non-bonded interactions are turn… --- ## [Number of coordinates did not match in coordinated file with the topology file](https://gromacs.bioexcel.eu/t/number-of-coordinates-did-not-match-in-coordinated-file-with-the-topology-file/1931)
**Author:** [@15\_123](https://gromacs.bioexcel.eu/u/15_123)\ **Replies:** 24\ **Last updated:** [May 1, 2025, 3:53pm UTC](https://gromacs.bioexcel.eu/t/number-of-coordinates-did-not-match-in-coordinated-file-with-the-topology-file/1931 "2025-05-01T15:53:02Z")
GROMACS version: 2021 GROMACS modification: Yes/No Here post your question Hello While performing protein-ligand interaction I encountered this fatal error saying that my coordinate numbers in coordinate file did not… --- ## [No default bond types, rykaert bell types and more](https://gromacs.bioexcel.eu/t/no-default-bond-types-rykaert-bell-types-and-more/11773)
**Author:** [@shris](https://gromacs.bioexcel.eu/u/shris)\ **Replies:** 1\ **Last updated:** [March 24, 2025, 10:06am UTC](https://gromacs.bioexcel.eu/t/no-default-bond-types-rykaert-bell-types-and-more/11773 "2025-03-24T10:06:12Z")
GROMACS version:gmx grompp, version 2019.5 GROMACS modification: Yes/No I keep getting the error for no default bond types, no default rykaert bell types and more. For the monomer, I got this very error, turns out the … --- ## [No default Position Rest. graphene sheet](https://gromacs.bioexcel.eu/t/no-default-position-rest-graphene-sheet/11756)
**Author:** [@bsh83](https://gromacs.bioexcel.eu/u/bsh83)\ **Replies:** 0\ **Last updated:** [March 16, 2025, 1:34pm UTC](https://gromacs.bioexcel.eu/t/no-default-position-rest-graphene-sheet/11756 "2025-03-16T13:34:22Z")
GROMACS version: GROMACS modification: Yes/No Here post your question hello every body, I want simulate tetramer of chitosan and a graphene sheet in tip3p water.the charm gui was create the itp files and I have posit… --- ## [\[MD Simulation Error\] Fatal PME Rank Issue: Particles Moving Out of Domain Decomposition Cell](https://gromacs.bioexcel.eu/t/md-simulation-error-fatal-pme-rank-issue-particles-moving-out-of-domain-decomposition-cell/11670)
**Author:** [@raj](https://gromacs.bioexcel.eu/u/raj)\ **Replies:** 2\ **Last updated:** [March 4, 2025, 9:51am UTC](https://gromacs.bioexcel.eu/t/md-simulation-error-fatal-pme-rank-issue-particles-moving-out-of-domain-decomposition-cell/11670 "2025-03-04T09:51:18Z")
GROMACS version: VERSION 2023.3-plumed\_2.9.0 I am running a GROMACS simulation of 7.5millions all-atoms using gmx mdrun (version 2023.3-plumed\_2.9.0) with MPI parallelization (40 ranks), and I encountered the following … --- ## [The largest distance between excluded atoms is 1.725 nm, which is larger than the cut-off distance](https://gromacs.bioexcel.eu/t/the-largest-distance-between-excluded-atoms-is-1-725-nm-which-is-larger-than-the-cut-off-distance/4153)
**Author:** [@PSS67](https://gromacs.bioexcel.eu/u/PSS67)\ **Replies:** 17\ **Last updated:** [February 5, 2025, 3:12pm UTC](https://gromacs.bioexcel.eu/t/the-largest-distance-between-excluded-atoms-is-1-725-nm-which-is-larger-than-the-cut-off-distance/4153 "2025-02-05T15:12:48Z")
GROMACS version: 2022.1 GROMACS modification: No When using editconf to make a box from a crystal lattice (4x4x4 unit cells) and using a gro file which is fine, I get a new gro file where there are some bad H-H interac… --- ## ["No default Bond types" error during grompp for specbond.dat bonds](https://gromacs.bioexcel.eu/t/no-default-bond-types-error-during-grompp-for-specbond-dat-bonds/11402)
**Author:** [@shahina](https://gromacs.bioexcel.eu/u/shahina)\ **Replies:** 0\ **Last updated:** [January 29, 2025, 8:36am UTC](https://gromacs.bioexcel.eu/t/no-default-bond-types-error-during-grompp-for-specbond-dat-bonds/11402 "2025-01-29T08:36:08Z")
GROMACS version: 2023.3 GROMACS modification: No I have tried to create a non-natural amino acid for incorporation into a peptide backbone. The non-natural amino acid is essentially a cysteine with an attached benzene … --- ## [No default U-B Types](https://gromacs.bioexcel.eu/t/no-default-u-b-types/11047)
**Author:** [@cboeckergrieme](https://gromacs.bioexcel.eu/u/cboeckergrieme)\ **Replies:** 0\ **Last updated:** [January 16, 2025, 3:47am UTC](https://gromacs.bioexcel.eu/t/no-default-u-b-types/11047 "2025-01-16T03:47:01Z")
GROMACS version: 2024.2 GROMACS modification: No Hello, I’m trying to simulate a lipid bilayer built by charmm-gui. When trying to create the ions.tpr file using gmx grompp and the files ions.mdp, solv.gro, and topol.t… --- ## [Warning: atom name in .top and .gro does not match](https://gromacs.bioexcel.eu/t/warning-atom-name-in-top-and-gro-does-not-match/11110)
**Author:** [@khainhienluu](https://gromacs.bioexcel.eu/u/khainhienluu)\ **Replies:** 2\ **Last updated:** [January 23, 2025, 6:14pm UTC](https://gromacs.bioexcel.eu/t/warning-atom-name-in-top-and-gro-does-not-match/11110 "2025-01-23T18:14:11Z")
GROMACS version: 2024.4 GROMACS modification: No I’m building a coarse-grain (MARTINI) model of lipid droplet. My process is first build a small part (1/27) of the droplet and then use insert-molecules to make the full… --- ## [Invalid order for directive atomtypes (error)](https://gromacs.bioexcel.eu/t/invalid-order-for-directive-atomtypes-error/3859)
**Author:** [@merry](https://gromacs.bioexcel.eu/u/merry)\ **Replies:** 17\ **Last updated:** [January 13, 2025, 12:11pm UTC](https://gromacs.bioexcel.eu/t/invalid-order-for-directive-atomtypes-error/3859 "2025-01-13T12:11:56Z")
GROMACS version: 2019.4 GROMACS modification: No Here post your question Hi GMX users, In my studied system there are 2 types of small molecules (LIG and POV). I prepared the itp files for them using antechamber modu… --- ## [No default improper dihedral types in Amber ff14sb-OL21 for DNA simulations](https://gromacs.bioexcel.eu/t/no-default-improper-dihedral-types-in-amber-ff14sb-ol21-for-dna-simulations/10813)
**Author:** [@TGaziri](https://gromacs.bioexcel.eu/u/TGaziri)\ **Replies:** 2\ **Last updated:** [December 22, 2024, 12:33am UTC](https://gromacs.bioexcel.eu/t/no-default-improper-dihedral-types-in-amber-ff14sb-ol21-for-dna-simulations/10813 "2024-12-22T00:33:12Z")
GROMACS version: 2022.4 GROMACS modification: No Hello, I’m trying to set up a DNA simulation with Amber OL21, using the Gromacs port of the ff14sb-OL21 forcefield. But after I created the topology I got a bunch of th… --- ## [Error: Topol.top file doesn\`t match solv.gro file](https://gromacs.bioexcel.eu/t/error-topol-top-file-doesn-t-match-solv-gro-file/10852)
**Author:** [@emiliakasi](https://gromacs.bioexcel.eu/u/emiliakasi)\ **Replies:** 1\ **Last updated:** [December 18, 2024, 4:45pm UTC](https://gromacs.bioexcel.eu/t/error-topol-top-file-doesn-t-match-solv-gro-file/10852 "2024-12-18T16:45:17Z")
GROMACS version: Jul2022 GROMACS modification: Yes/No Here post your question Good evening , dr Im EmiliaKasi here, a researcher who is currently running MD simulation using the GROMACS by adhering to the online tuto… --- ## [Issues with MD Run and Fe Displacement in Hemoglobin Simulation](https://gromacs.bioexcel.eu/t/issues-with-md-run-and-fe-displacement-in-hemoglobin-simulation/10616)
**Author:** [@akanksha\_bhosale](https://gromacs.bioexcel.eu/u/akanksha_bhosale)\ **Replies:** 4\ **Last updated:** [December 13, 2024, 4:45am UTC](https://gromacs.bioexcel.eu/t/issues-with-md-run-and-fe-displacement-in-hemoglobin-simulation/10616 "2024-12-13T04:45:10Z")
GROMACS version:2022 GROMACS modification: Yes/No I am performing a molecular dynamics simulation of hemoglobin using the GROMOS54a7 force field, as it generates topology parameters for the heme group. While most of th… --- ## [ERROR 164 \[file topol.top, line 100195\]: No default Ryckaert-Bell. types](https://gromacs.bioexcel.eu/t/error-164-file-topol-top-line-100195-no-default-ryckaert-bell-types/10660)
**Author:** [@vardhan](https://gromacs.bioexcel.eu/u/vardhan)\ **Replies:** 3\ **Last updated:** [November 29, 2024, 11:33am UTC](https://gromacs.bioexcel.eu/t/error-164-file-topol-top-line-100195-no-default-ryckaert-bell-types/10660 "2024-11-29T11:33:42Z")
GROMACS version: 2020.1 GROMACS modification: No Hi all, I am trying to simulate a system with triethyl citrate molecule. Initially I built the molecule by mapping the atoms to the opls\_aa atom types. I modified the r… --- ## [Energy minimization error sc-r-power = 48 not supported](https://gromacs.bioexcel.eu/t/energy-minimization-error-sc-r-power-48-not-supported/6165)
**Author:** [@Gupta](https://gromacs.bioexcel.eu/u/Gupta)\ **Replies:** 4\ **Last updated:** [November 18, 2024, 7:43am UTC](https://gromacs.bioexcel.eu/t/energy-minimization-error-sc-r-power-48-not-supported/6165 "2024-11-18T07:43:33Z")
GROMACS version: GROMACS modification: Yes/No Here post your question Dear Gromacs Community, I am getting the following error during energy minimization of my system using Gromacs 2022.1 version. I appreciate your h… --- ## [Ligand MD simulation](https://gromacs.bioexcel.eu/t/ligand-md-simulation/10503)
**Author:** [@nhina](https://gromacs.bioexcel.eu/u/nhina)\ **Replies:** 2\ **Last updated:** [November 8, 2024, 8:35am UTC](https://gromacs.bioexcel.eu/t/ligand-md-simulation/10503 "2024-11-08T08:35:05Z")
GROMACS version: 2019.6 Hi guys, I am performing a MD simulation for ligand only in the FEP calculations framework. The ligand molecules are parameterized by ATP website for gromos force field. Now, I get error about f… --- ## [Grompp errors with v2024.3: The drift estimate should be a finite value](https://gromacs.bioexcel.eu/t/grompp-errors-with-v2024-3-the-drift-estimate-should-be-a-finite-value/10437)
**Author:** [@arfinney](https://gromacs.bioexcel.eu/u/arfinney)\ **Replies:** 5\ **Last updated:** [October 30, 2024, 8:17am UTC](https://gromacs.bioexcel.eu/t/grompp-errors-with-v2024-3-the-drift-estimate-should-be-a-finite-value/10437 "2024-10-30T08:17:10Z")
GROMACS version: 2024.3 GROMACS modification: No Having installed the latest version of gmx, I get a grommp error on input files that work fine with previous versions: Program: gmx grompp, version 2024.3 Source fi… --- ## [Fatal error: Syntax error - File ffnonbonded.itp, line 5 Last line read: '\[ atomtypes \]' Invalid ord](https://gromacs.bioexcel.eu/t/fatal-error-syntax-error-file-ffnonbonded-itp-line-5-last-line-read-atomtypes-invalid-ord/10427)
**Author:** [@Arbazattar11](https://gromacs.bioexcel.eu/u/Arbazattar11)\ **Replies:** 5\ **Last updated:** [October 29, 2024, 1:18pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-syntax-error-file-ffnonbonded-itp-line-5-last-line-read-atomtypes-invalid-ord/10427 "2024-10-29T13:18:52Z")
GROMACS version: 2023.1-Ubuntu\_2023.1\_2ubuntu1 GROMACS modification: Yes Here post your question ; This force field generated by charmm2gmx.py from ; multiple charmm parameter files ; and multiple charmm topology fi… [Next page](https://gromacs.bioexcel.eu/tag/grompp/7.md?match_all_tags=true&page=1&tags%5B%5D=grompp)