# \#mdrun **URL:** https://gromacs.bioexcel.eu/tag/mdrun/8.md [Latest](https://gromacs.bioexcel.eu/latest.md) · [Categories](https://gromacs.bioexcel.eu/categories.md) · [Tags](https://gromacs.bioexcel.eu/tags.md) --- ## [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): … --- ## [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… --- ## [MDrun: Simulation speed jumping a factor of 10 with a gpu executable](https://gromacs.bioexcel.eu/t/mdrun-simulation-speed-jumping-a-factor-of-10-with-a-gpu-executable/13676)
**Author:** [@zaidi1](https://gromacs.bioexcel.eu/u/zaidi1)\ **Replies:** 6\ **Last updated:** [August 24, 2026, 1:28pm UTC](https://gromacs.bioexcel.eu/t/mdrun-simulation-speed-jumping-a-factor-of-10-with-a-gpu-executable/13676 "2026-08-24T13:28:02Z")
GROMACS version: 2025.3 GROMACS modification: No My simulations on a GPU partition in our HPC cluster are behaving erratically. I see a sudden drop in my simulation speed by a factor of 10, where separate runs fluctuat… --- ## [Loss of performance in v. 2021](https://gromacs.bioexcel.eu/t/loss-of-performance-in-v-2021/3323)
**Author:** [@Sasha](https://gromacs.bioexcel.eu/u/Sasha)\ **Replies:** 27\ **Last updated:** [August 24, 2026, 8:43am UTC](https://gromacs.bioexcel.eu/t/loss-of-performance-in-v-2021/3323 "2026-08-24T08:43:13Z")
Hi all, I have a small test system (~17K atoms) that contains nothing special: a solid membrane with a hole (membrane position-restrained at the edges), a string of periodic DNA, water, and some ions. The machine is 44-… --- ## ["Accelerating molecular dynamics simulations using fast Ewald summation with prolates" paper](https://gromacs.bioexcel.eu/t/accelerating-molecular-dynamics-simulations-using-fast-ewald-summation-with-prolates-paper/13563)
**Author:** [@Michael\_Shirts](https://gromacs.bioexcel.eu/u/Michael_Shirts)\ **Replies:** 6\ **Last updated:** [August 13, 2026, 3:03pm UTC](https://gromacs.bioexcel.eu/t/accelerating-molecular-dynamics-simulations-using-fast-ewald-summation-with-prolates-paper/13563 "2026-08-13T15:03:02Z")
An interesting paper in Nature Communications proposing a new way to do Ewald summation that appears better/faster/scales better than PME. They said they had implemented it in GROMACS - I wonder if developers have been … --- ## [RTX 5070 Not Utilized](https://gromacs.bioexcel.eu/t/rtx-5070-not-utilized/11986)
**Author:** [@crumble](https://gromacs.bioexcel.eu/u/crumble)\ **Replies:** 3\ **Last updated:** [August 1, 2026, 5:14am UTC](https://gromacs.bioexcel.eu/t/rtx-5070-not-utilized/11986 "2026-08-01T05:14:19Z")
GROMACS version: 2024.2 GROMACS modification: No I’ve recently built a new workstation running Linux Mint 22.1 based around an RTX 5070 card. I’ve installed the Nvidia 570.133.07 open source drivers through the Ubuntu … --- ## [Multiple gmx processes on GPU(s) ran too slowly](https://gromacs.bioexcel.eu/t/multiple-gmx-processes-on-gpu-s-ran-too-slowly/13535)
**Author:** [@HoaThanhLe](https://gromacs.bioexcel.eu/u/HoaThanhLe)\ **Replies:** 10\ **Last updated:** [July 13, 2026, 1:08pm UTC](https://gromacs.bioexcel.eu/t/multiple-gmx-processes-on-gpu-s-ran-too-slowly/13535 "2026-07-13T13:08:16Z")
GROMACS version: 2026.0 (Anaconda distribution, build nompi\_cuda\_h39c90b0\_1, channel conda-forge) GROMACS modification: No Hello, I need to simulate several systems almost identical in terms of the number of atoms. All… --- ## [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… --- ## [WT vs mutant protein-protein complex MD: should mutant be generated from WT docked complex or redock](https://gromacs.bioexcel.eu/t/wt-vs-mutant-protein-protein-complex-md-should-mutant-be-generated-from-wt-docked-complex-or-redock/13529)
**Author:** [@SBanerjee](https://gromacs.bioexcel.eu/u/SBanerjee)\ **Replies:** 0\ **Last updated:** [June 15, 2026, 11:12am UTC](https://gromacs.bioexcel.eu/t/wt-vs-mutant-protein-protein-complex-md-should-mutant-be-generated-from-wt-docked-complex-or-redock/13529 "2026-06-15T11:12:09Z")
GROMACS version: 2026 GROMACS modification:No Here post your question: I am working on MD simulations of wild-type p53 and mutant p53 protein-protein complexes. For the wild-type p53 system, I performed protein-prote… --- ## [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… --- ## [Box changing shape after equilibration](https://gromacs.bioexcel.eu/t/box-changing-shape-after-equilibration/13458)
**Author:** [@nysh](https://gromacs.bioexcel.eu/u/nysh)\ **Replies:** 8\ **Last updated:** [May 26, 2026, 3:08pm UTC](https://gromacs.bioexcel.eu/t/box-changing-shape-after-equilibration/13458 "2026-05-26T15:08:13Z")
GROMACS version: 2024.4 GROMACS modification: No Hello! I ran into a situation with my simulations and I was wondering if anyone would have some wisdom as to what is causing this strange phenomenon. I create a protei… --- ## [How to solve inconsistent shifts over periodic boundaries in protein-dna run in minimization step?](https://gromacs.bioexcel.eu/t/how-to-solve-inconsistent-shifts-over-periodic-boundaries-in-protein-dna-run-in-minimization-step/1758)
**Author:** [@ladimafakher](https://gromacs.bioexcel.eu/u/ladimafakher)\ **Replies:** 11\ **Last updated:** [May 17, 2026, 2:45pm UTC](https://gromacs.bioexcel.eu/t/how-to-solve-inconsistent-shifts-over-periodic-boundaries-in-protein-dna-run-in-minimization-step/1758 "2026-05-17T14:45:00Z")
GROMACS version:2021 GROMACS modification: No Hi, I want to run a protein-DNA complex with Amber force field in Gromacs. I got this error in the minimization step. what is this problem and how can I solve it? Fatal er… --- ## [Segmentation fault without further information](https://gromacs.bioexcel.eu/t/segmentation-fault-without-further-information/13448)
**Author:** [@jm.gomez](https://gromacs.bioexcel.eu/u/jm.gomez)\ **Replies:** 3\ **Last updated:** [May 13, 2026, 9:19am UTC](https://gromacs.bioexcel.eu/t/segmentation-fault-without-further-information/13448 "2026-05-13T09:19:35Z")
GROMACS version: 2025.4-conda\_forge GROMACS modification: No Hi, I am trying to simulate a Self-Assembly Monolayer. I have followed what I understand are standard steps: Box creation, Energy minimisation, NVT process… --- ## [Colvars: Error: keyword "customfunction" is not supported](https://gromacs.bioexcel.eu/t/colvars-error-keyword-customfunction-is-not-supported/8925)
**Author:** [@fmytreberg](https://gromacs.bioexcel.eu/u/fmytreberg)\ **Replies:** 3\ **Last updated:** [May 12, 2026, 3:10am UTC](https://gromacs.bioexcel.eu/t/colvars-error-keyword-customfunction-is-not-supported/8925 "2026-05-12T03:10:18Z")
GROMACS version: 2024.1 GROMACS modification: Yes/No I’m new posting in the forum, but a long time GROMACS user. I have been working with the colvars module as implemented in GROMACS 2024.1 and am having problems with … --- ## [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 … --- ## [Mdrun with awh for a dimeric protein](https://gromacs.bioexcel.eu/t/mdrun-with-awh-for-a-dimeric-protein/13428)
**Author:** [@csnail](https://gromacs.bioexcel.eu/u/csnail)\ **Replies:** 0\ **Last updated:** [April 29, 2026, 11:35am UTC](https://gromacs.bioexcel.eu/t/mdrun-with-awh-for-a-dimeric-protein/13428 "2026-04-29T11:35:40Z")
GROMACS version: 2025.3 GROMACS modification: No, just the MPI library. I’m currently researching the dimerization of a fragment of zinc-finger protein (calculations are made for two coupled identical chains of 68 amin… --- ## [Energy calculations during mdrun with multiple groups](https://gromacs.bioexcel.eu/t/energy-calculations-during-mdrun-with-multiple-groups/13406)
**Author:** [@luana.frco](https://gromacs.bioexcel.eu/u/luana.frco)\ **Replies:** 2\ **Last updated:** [April 23, 2026, 11:45pm UTC](https://gromacs.bioexcel.eu/t/energy-calculations-during-mdrun-with-multiple-groups/13406 "2026-04-23T23:45:38Z")
GROMACS version: 2024.1 GROMACS modification: No Greetings, everyone! I have a perhaps less practical question that I am hoping someone can help me with. I am having trouble understanding the energy calculations (and … --- ## [Extreme performance loss with version 2026.1 on APUs](https://gromacs.bioexcel.eu/t/extreme-performance-loss-with-version-2026-1-on-apus/13350)
**Author:** [@Florian\_Leidner](https://gromacs.bioexcel.eu/u/Florian_Leidner)\ **Replies:** 10\ **Last updated:** [April 13, 2026, 12:31pm UTC](https://gromacs.bioexcel.eu/t/extreme-performance-loss-with-version-2026-1-on-apus/13350 "2026-04-13T12:31:14Z")
GROMACS version: 2026.1 GROMACS modification: No Dear all, I want to ask the community for help with an issue i encountered when running simulations on APUs. I am running these simulation on a HPC system where each n… --- ## [GROMACS Command for Minimization, Equilibration, Production Runs from CHARMM README](https://gromacs.bioexcel.eu/t/gromacs-command-for-minimization-equilibration-production-runs-from-charmm-readme/13358)
**Author:** [@urtig](https://gromacs.bioexcel.eu/u/urtig)\ **Replies:** 0\ **Last updated:** [April 4, 2026, 3:19am UTC](https://gromacs.bioexcel.eu/t/gromacs-command-for-minimization-equilibration-production-runs-from-charmm-readme/13358 "2026-04-04T03:19:19Z")
GROMACS version: 2023.4 GROMACS modification: No Here post your question Hi guys I’m running gromacs on a computing cluster using SLURM. I have generated the Charmmgui webserver files and and are shown below. -toppar … --- ## [Abnormal dVremain/dl values in GROMACS 2025.0 with vdw-type=pme and free-energy](https://gromacs.bioexcel.eu/t/abnormal-dvremain-dl-values-in-gromacs-2025-0-with-vdw-type-pme-and-free-energy/13344)
**Author:** [@donghwanz](https://gromacs.bioexcel.eu/u/donghwanz)\ **Replies:** 3\ **Last updated:** [March 31, 2026, 6:39am UTC](https://gromacs.bioexcel.eu/t/abnormal-dvremain-dl-values-in-gromacs-2025-0-with-vdw-type-pme-and-free-energy/13344 "2026-03-31T06:39:16Z")
GROMACS version: 2025.0 (bug) / 2024.4 (normal) GROMACS modification: No I found a potential bug in GROMACS 2025.0 related to free energy calculations with LJ-PME (vdw-type=pme). Symptom: GROMACS 2024.4: dVremain/d… --- ## [Issues regarding MDrun in HPC](https://gromacs.bioexcel.eu/t/issues-regarding-mdrun-in-hpc/13330)
**Author:** [@urtig](https://gromacs.bioexcel.eu/u/urtig)\ **Replies:** 0\ **Last updated:** [March 26, 2026, 4:10am UTC](https://gromacs.bioexcel.eu/t/issues-regarding-mdrun-in-hpc/13330 "2026-03-26T04:10:39Z")
Hi all, I am done creating my topologies from CHARMMGUI, the issue is I can’t seem to run the my MD run in GROMACS using an HPC --- ## [Coulomb (SR) calculation in PME](https://gromacs.bioexcel.eu/t/coulomb-sr-calculation-in-pme/13301)
**Author:** [@shaunak](https://gromacs.bioexcel.eu/u/shaunak)\ **Replies:** 9\ **Last updated:** [March 19, 2026, 4:23pm UTC](https://gromacs.bioexcel.eu/t/coulomb-sr-calculation-in-pme/13301 "2026-03-19T16:23:31Z")
Hi, I’m trying to understand the calculation of Coulomb (SR) in an alanine dipeptide molecule. In my effort to do so, I read documentation and came across this statement ( Long Range Electrostatics - GROMACS 2026.1 docu… --- ## [Steered Molecular dynamics of a ligand moving towards bilayer membrane](https://gromacs.bioexcel.eu/t/steered-molecular-dynamics-of-a-ligand-moving-towards-bilayer-membrane/13288)
**Author:** [@Ranbir720](https://gromacs.bioexcel.eu/u/Ranbir720)\ **Replies:** 1\ **Last updated:** [March 16, 2026, 9:59am UTC](https://gromacs.bioexcel.eu/t/steered-molecular-dynamics-of-a-ligand-moving-towards-bilayer-membrane/13288 "2026-03-16T09:59:31Z")
GROMACS version: 2025.3 GROMACS modification: No ; Pull code pull = yes pull\_ncoords = 1 ; only one reaction coordinate pull\_ngroups = 2 ; two groups defining… --- ## [Paradoxical Density in OPLS-AA: Diesel mixture density is abnormally LOWER than its lightest compone](https://gromacs.bioexcel.eu/t/paradoxical-density-in-opls-aa-diesel-mixture-density-is-abnormally-lower-than-its-lightest-compone/13303)
**Author:** [@scorpion1028](https://gromacs.bioexcel.eu/u/scorpion1028)\ **Replies:** 6\ **Last updated:** [March 15, 2026, 4:58am UTC](https://gromacs.bioexcel.eu/t/paradoxical-density-in-opls-aa-diesel-mixture-density-is-abnormally-lower-than-its-lightest-compone/13303 "2026-03-15T04:58:54Z")
GROMACS version:2022.03 GROMACS modification: Yes/No Here post your question Dear GROMACS Community, I am currently working on simulating a complex diesel surrogate fuel system (a mixture of various hydrocarbons rang… --- ## [Restart MD run from a particular time moment in \*.xtc file?](https://gromacs.bioexcel.eu/t/restart-md-run-from-a-particular-time-moment-in-xtc-file/13269)
**Author:** [@wswgg](https://gromacs.bioexcel.eu/u/wswgg)\ **Replies:** 5\ **Last updated:** [March 6, 2026, 5:50pm UTC](https://gromacs.bioexcel.eu/t/restart-md-run-from-a-particular-time-moment-in-xtc-file/13269 "2026-03-06T17:50:00Z")
Hello, dear GROMACS users & developers! It happened that one of my GROMACS jobs was not finalised properly. As a result, I have the log, gro, edr, cpt, tpr files corresponding to the end of the simulation \[ 1.5 ms \] , b… --- ## [Gromacs-CP2k energy minimization](https://gromacs.bioexcel.eu/t/gromacs-cp2k-energy-minimization/13241)
**Author:** [@krsiwa](https://gromacs.bioexcel.eu/u/krsiwa)\ **Replies:** 0\ **Last updated:** [February 24, 2026, 12:08pm UTC](https://gromacs.bioexcel.eu/t/gromacs-cp2k-energy-minimization/13241 "2026-02-24T12:08:43Z")
Hi everyone, I am trying to perform a QM/MM geometry optimization after an MD simulation using the Gromacs-Cp2k interface. I would like to use the L-BFGS integrator for minimization, but I receive the following error: F… --- ## [Steered MD Simulation error](https://gromacs.bioexcel.eu/t/steered-md-simulation-error/13144)
**Author:** [@Aneesha.A](https://gromacs.bioexcel.eu/u/Aneesha.A)\ **Replies:** 19\ **Last updated:** [February 19, 2026, 3:24pm UTC](https://gromacs.bioexcel.eu/t/steered-md-simulation-error/13144 "2026-02-19T15:24:06Z")
GROMACS version: 2021.4/gpuvolta GROMACS modification: No Hi everyone, I am following Tutorial 3: Umbrella Sampling, but altering the .mdp files to a method section from a paper (unfortunately the authors are not much… --- ## [Equilibration not work](https://gromacs.bioexcel.eu/t/equilibration-not-work/13223)
**Author:** [@gluizcar](https://gromacs.bioexcel.eu/u/gluizcar)\ **Replies:** 0\ **Last updated:** [February 17, 2026, 1:52pm UTC](https://gromacs.bioexcel.eu/t/equilibration-not-work/13223 "2026-02-17T13:52:46Z")
GROMACS version: 2022 GROMACS modification: NoHi every one. I have this system, jannus MoSSe, with nanopore passivated with H atoms. I generated my force field files via acpype. I tried, many times, to simulation my s… --- ## [Issue with orienting two monomers during dimer insertion in GoMARTINI membrane system](https://gromacs.bioexcel.eu/t/issue-with-orienting-two-monomers-during-dimer-insertion-in-gomartini-membrane-system/13216)
**Author:** [@Rudhra](https://gromacs.bioexcel.eu/u/Rudhra)\ **Replies:** 0\ **Last updated:** [February 13, 2026, 3:38pm UTC](https://gromacs.bioexcel.eu/t/issue-with-orienting-two-monomers-during-dimer-insertion-in-gomartini-membrane-system/13216 "2026-02-13T15:38:56Z")
GROMACS version: GROMACS modification: Yes/No Here post your question Hello, I am investigating dimer formation of a membrane protein using a coarse-grained GoMARTINI model in a neuronal membrane system. System setu… [Next page](https://gromacs.bioexcel.eu/tag/mdrun/8.md?match_all_tags=true&page=1&tags%5B%5D=mdrun)