# \#mdrun-performance **URL:** https://gromacs.bioexcel.eu/tag/mdrun-performance/33.md [Latest](https://gromacs.bioexcel.eu/latest.md) · [Categories](https://gromacs.bioexcel.eu/categories.md) · [Tags](https://gromacs.bioexcel.eu/tags.md) --- ## [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… --- ## [Keywords in command line for getting good performance in gromacs](https://gromacs.bioexcel.eu/t/keywords-in-command-line-for-getting-good-performance-in-gromacs/7486)
**Author:** [@SarthakTrivedi](https://gromacs.bioexcel.eu/u/SarthakTrivedi)\ **Replies:** 3\ **Last updated:** [November 23, 2025, 1:35pm UTC](https://gromacs.bioexcel.eu/t/keywords-in-command-line-for-getting-good-performance-in-gromacs/7486 "2025-11-23T13:35:48Z")
I am trying to run gromacs 2023.2 gpu on HPC. I am getting super slow performance in HPC. I run the calculation for the test purpose on 8 cores for 10 mins only. The projected steps of calculation is about 15,000 in 10 m… --- ## [Performance of SMD simulation](https://gromacs.bioexcel.eu/t/performance-of-smd-simulation/12748)
**Author:** [@mpedraza](https://gromacs.bioexcel.eu/u/mpedraza)\ **Replies:** 1\ **Last updated:** [October 10, 2025, 8:51am UTC](https://gromacs.bioexcel.eu/t/performance-of-smd-simulation/12748 "2025-10-10T08:51:40Z")
GROMACS version: 2024.3-plumed\_2.9.3 GROMACS modification: Yes/No I want to know if there is a way to find out the performance (ns/day) I am getting for my system by the end of an SMD when it fails due to box size cons… --- ## [Unexplained calculation stalling during density fit](https://gromacs.bioexcel.eu/t/unexplained-calculation-stalling-during-density-fit/12449)
**Author:** [@YannLefrancois](https://gromacs.bioexcel.eu/u/YannLefrancois)\ **Replies:** 2\ **Last updated:** [August 25, 2025, 1:03pm UTC](https://gromacs.bioexcel.eu/t/unexplained-calculation-stalling-during-density-fit/12449 "2025-08-25T13:03:48Z")
GROMACS version: 2024.4=mpi\_openmpi\_cuda\_he6b8466\_0 (conda distribution) GROMACS modification: Yes/No I’m trying to do density fitting, following the bioexcel webinar #82, when i look at my performance log I see this … --- ## [Guidance on Identifying CPU vs. GPU Bottlenecks in GROMACS Simulations](https://gromacs.bioexcel.eu/t/guidance-on-identifying-cpu-vs-gpu-bottlenecks-in-gromacs-simulations/12289)
**Author:** [@ivangreg](https://gromacs.bioexcel.eu/u/ivangreg)\ **Replies:** 8\ **Last updated:** [July 3, 2025, 9:06pm UTC](https://gromacs.bioexcel.eu/t/guidance-on-identifying-cpu-vs-gpu-bottlenecks-in-gromacs-simulations/12289 "2025-07-03T21:06:18Z")
GROMACS version: 2025.2 GROMACS modification: No Here post your question Dear GROMACS Community, I hope this message finds you well. I am currently running simulations and am trying to determine whether my runs are b… --- ## [Optimizing Production Run with GPUs and CHARMM36](https://gromacs.bioexcel.eu/t/optimizing-production-run-with-gpus-and-charmm36/11623)
**Author:** [@b-omics](https://gromacs.bioexcel.eu/u/b-omics)\ **Replies:** 3\ **Last updated:** [February 27, 2025, 3:05pm UTC](https://gromacs.bioexcel.eu/t/optimizing-production-run-with-gpus-and-charmm36/11623 "2025-02-27T15:05:54Z")
GROMACS version: 2024.4 GROMACS modification: Yes/No I am simulating a system of approximately 330,000 atoms using CHARMM36 and aiming to significantly improve the performance of my production run. Currently, I am util… --- ## [Expanded ensemble: Performance impact of perturbing more atoms](https://gromacs.bioexcel.eu/t/expanded-ensemble-performance-impact-of-perturbing-more-atoms/11099)
**Author:** [@BjarneF](https://gromacs.bioexcel.eu/u/BjarneF)\ **Replies:** 4\ **Last updated:** [January 23, 2025, 6:30pm UTC](https://gromacs.bioexcel.eu/t/expanded-ensemble-performance-impact-of-perturbing-more-atoms/11099 "2025-01-23T18:30:35Z")
GROMACS version: 2024.1 GROMACS modification: No Hi all, I am trying to understand the ways in which the performance of expanded ensemble simulations worsens with increasing system size and with larger numbers of atom… --- ## [Hardware advice for maximizing throughput (CpHMD/Replica Exchange)](https://gromacs.bioexcel.eu/t/hardware-advice-for-maximizing-throughput-cphmd-replica-exchange/11024)
**Author:** [@valgu](https://gromacs.bioexcel.eu/u/valgu)\ **Replies:** 0\ **Last updated:** [January 13, 2025, 4:21pm UTC](https://gromacs.bioexcel.eu/t/hardware-advice-for-maximizing-throughput-cphmd-replica-exchange/11024 "2025-01-13T16:21:25Z")
GROMACS version: 2021-beta1-plumed-2.9.2-dev-UNCHECKED GROMACS modification: Yes Dear Gromacs community, I have some questions regarding the hardware for running Replica Exchange. After doing some benchmarks on VMs an… --- ## [Domain decomposition error + Setting MPI ranks compatible with custom domains](https://gromacs.bioexcel.eu/t/domain-decomposition-error-setting-mpi-ranks-compatible-with-custom-domains/2048)
**Author:** [@woutervv](https://gromacs.bioexcel.eu/u/woutervv)\ **Replies:** 2\ **Last updated:** [October 30, 2024, 7:11am UTC](https://gromacs.bioexcel.eu/t/domain-decomposition-error-setting-mpi-ranks-compatible-with-custom-domains/2048 "2024-10-30T07:11:28Z")
GROMACS version: GROMACS/2020-foss-2019b and GROMACS/2021-foss-2020b GROMACS modification: Yes (HPC installations, info in linked log file) Dear all, I am simulating a protein-ligand complex in a rhombic dodecahedral … --- ## [AVX2 on Ryzen: What should I look for?](https://gromacs.bioexcel.eu/t/avx2-on-ryzen-what-should-i-look-for/9624)
**Author:** [@a.hazarika](https://gromacs.bioexcel.eu/u/a.hazarika)\ **Replies:** 2\ **Last updated:** [August 21, 2024, 6:42pm UTC](https://gromacs.bioexcel.eu/t/avx2-on-ryzen-what-should-i-look-for/9624 "2024-08-21T18:42:58Z")
GROMACS version: 2023.5 GROMACS modification: No The question I originally had was about the performance difference I had in between two 8-core CPUs: a Ryzen 1700 on my own desktop versus a Xeon Silver 4208. Looking up… --- ## [Optimizing Selection of RTX 40 Series GPUs: Evaluating Performance and Cost Efficiency](https://gromacs.bioexcel.eu/t/optimizing-selection-of-rtx-40-series-gpus-evaluating-performance-and-cost-efficiency/9247)
**Author:** [@RaedKhashan](https://gromacs.bioexcel.eu/u/RaedKhashan)\ **Replies:** 6\ **Last updated:** [June 6, 2024, 7:35pm UTC](https://gromacs.bioexcel.eu/t/optimizing-selection-of-rtx-40-series-gpus-evaluating-performance-and-cost-efficiency/9247 "2024-06-06T19:35:27Z")
Hello GROMACS Users, Does anyone know the “extent” to which the type and memory of RTX 40 series GPUs affect simulation performance? Currently, the price differences are substantial; for instance, the 4060Ti-8GB costs $… --- ## [Scaling problem for very large systems](https://gromacs.bioexcel.eu/t/scaling-problem-for-very-large-systems/9178)
**Author:** [@Gusten](https://gromacs.bioexcel.eu/u/Gusten)\ **Replies:** 14\ **Last updated:** [May 29, 2024, 9:26am UTC](https://gromacs.bioexcel.eu/t/scaling-problem-for-very-large-systems/9178 "2024-05-29T09:26:43Z")
GROMACS version:2024.2 GROMACS modification: No I’m currently benchmarking gromacs against my own code (that operates in a significantly different way) for large scale particle simulation. I’m comparing an atomistic re… --- ## [Running Gromacs in HPC](https://gromacs.bioexcel.eu/t/running-gromacs-in-hpc/9150)
**Author:** [@Ligand1](https://gromacs.bioexcel.eu/u/Ligand1)\ **Replies:** 5\ **Last updated:** [May 17, 2024, 9:06am UTC](https://gromacs.bioexcel.eu/t/running-gromacs-in-hpc/9150 "2024-05-17T09:06:39Z")
GROMACS version: 2022.5 GROMACS modification: No Hi everyone! I am trying to optimize the duration of my simulations using Gromacs on a HPC cluster. I am using Lysozyme in water tutorial for this optimization exercise… --- ## [Low Gromacs Performance on WSL Environment](https://gromacs.bioexcel.eu/t/low-gromacs-performance-on-wsl-environment/8494)
**Author:** [@Felicia](https://gromacs.bioexcel.eu/u/Felicia)\ **Replies:** 4\ **Last updated:** [March 4, 2024, 2:35pm UTC](https://gromacs.bioexcel.eu/t/low-gromacs-performance-on-wsl-environment/8494 "2024-03-04T14:35:11Z")
GROMACS version: 2020.1-Ubuntu-2020.1-1 GROMACS modification: No Hi, I’m currently working on my Molecular Dynamics (MD) Simulation project using Gromacs in Windows Subsystem for Linux (WSL) Environment. My hardware is… --- ## [GROMACS performance on 8 cores workstation](https://gromacs.bioexcel.eu/t/gromacs-performance-on-8-cores-workstation/3477)
**Author:** [@alexmas](https://gromacs.bioexcel.eu/u/alexmas)\ **Replies:** 8\ **Last updated:** [February 20, 2024, 10:06am UTC](https://gromacs.bioexcel.eu/t/gromacs-performance-on-8-cores-workstation/3477 "2024-02-20T10:06:31Z")
GROMACS version: 2021.4 GROMACS modification: No Hello, I just completed a test run on a new installation and the performance was much lower then I expected: 0.661ns/day with a 41,175 Atoms system on an 8 cores CPU ha… --- ## [Scaling of MD with domain decomposition on JUWELS Cluster](https://gromacs.bioexcel.eu/t/scaling-of-md-with-domain-decomposition-on-juwels-cluster/8287)
**Author:** [@nitinmalapally](https://gromacs.bioexcel.eu/u/nitinmalapally)\ **Replies:** 2\ **Last updated:** [February 9, 2024, 8:48am UTC](https://gromacs.bioexcel.eu/t/scaling-of-md-with-domain-decomposition-on-juwels-cluster/8287 "2024-02-09T08:48:29Z")
GROMACS version: 2024-dev-20240201-787d96c7a9-unknown GROMACS modification: Yes I’m conducting some performance tests on the JUWELS Cluster, trying to see the improvement in performance that DD can bring within a singl… --- ## [Unevern spikes in RMSD graphs after MD simulations](https://gromacs.bioexcel.eu/t/unevern-spikes-in-rmsd-graphs-after-md-simulations/5944)
**Author:** [@gromacs\_amature](https://gromacs.bioexcel.eu/u/gromacs_amature)\ **Replies:** 5\ **Last updated:** [January 29, 2024, 11:36am UTC](https://gromacs.bioexcel.eu/t/unevern-spikes-in-rmsd-graphs-after-md-simulations/5944 "2024-01-29T11:36:30Z")
GROMACS version:GROMACS - gmx rms, VERSION 5.1.4 GROMACS modification: No Here post your question I followed the MD run tutorial from Gromacs. I have also applied position restrain for energy minimization. I chec… --- ## [The initial estimative of -nt \ parameter](https://gromacs.bioexcel.eu/t/the-initial-estimative-of-nt-int-parameter/7869)
**Author:** [@PabloLQFPP](https://gromacs.bioexcel.eu/u/PabloLQFPP)\ **Replies:** 0\ **Last updated:** [December 15, 2023, 11:52am UTC](https://gromacs.bioexcel.eu/t/the-initial-estimative-of-nt-int-parameter/7869 "2023-12-15T11:52:24Z")
GROMACS version: 2022.6 GROMACS modification: No Hi, community. I would like to know, how gromacs calculate an initial estimate for number of threads used on mdrun? For example, when run this command “gmx mdrun -deff… --- ## [A series of performance benchmarks for MD Apps, including GROMACS](https://gromacs.bioexcel.eu/t/a-series-of-performance-benchmarks-for-md-apps-including-gromacs/7078)
**Author:** [@Entropy\_YU](https://gromacs.bioexcel.eu/u/Entropy_YU)\ **Replies:** 17\ **Last updated:** [December 6, 2023, 5:32am UTC](https://gromacs.bioexcel.eu/t/a-series-of-performance-benchmarks-for-md-apps-including-gromacs/7078 "2023-12-06T05:32:58Z")
GROMACS version: 2023.2 GROMACS modification: No Title: Performance benchmarks for mainstream molecular dynamics simulation Apps on consumer GPUs from AMD, NVIDIA and Intel - Switch to AMD \[Part Ⅰ\] Link: http://bbs.k… --- ## [Are these timings fine?](https://gromacs.bioexcel.eu/t/are-these-timings-fine/7641)
**Author:** [@lutek14](https://gromacs.bioexcel.eu/u/lutek14)\ **Replies:** 3\ **Last updated:** [November 14, 2023, 12:23pm UTC](https://gromacs.bioexcel.eu/t/are-these-timings-fine/7641 "2023-11-14T12:23:33Z")
GROMACS version: gromacs/2021.4\_mpi\_plumed GROMACS modification: No Hello, I am running Gromacs on HPC for the first time, and I am unsure if the timings are fine. I am not sure whether I have allocated too many or to… --- ## [1 millisecond Coarse Grained simulation](https://gromacs.bioexcel.eu/t/1-millisecond-coarse-grained-simulation/7240)
**Author:** [@maialenzaze](https://gromacs.bioexcel.eu/u/maialenzaze)\ **Replies:** 2\ **Last updated:** [September 24, 2023, 2:05pm UTC](https://gromacs.bioexcel.eu/t/1-millisecond-coarse-grained-simulation/7240 "2023-09-24T14:05:06Z")
GROMACS version: GROMACS/2020.4-intel-2020a GROMACS modification: Yes Hi everyone! I’m attempting to do a millisecond to second range Coarse Grained MD with gromacs. I have both Martini22p and Martini3.0.0 systems of … --- ## [MD performance help using V\_100 GPU](https://gromacs.bioexcel.eu/t/md-performance-help-using-v-100-gpu/6613)
**Author:** [@pkoduro](https://gromacs.bioexcel.eu/u/pkoduro)\ **Replies:** 7\ **Last updated:** [June 21, 2023, 1:45pm UTC](https://gromacs.bioexcel.eu/t/md-performance-help-using-v-100-gpu/6613 "2023-06-21T13:45:30Z")
GROMACS version: 2021.5 GROMACS modification: No I have attempted various methods to enhance the simulation performance, but unfortunately, none have yielded positive results. I have included my log below. Would someon… --- ## [NVT memory error for free energy calculation](https://gromacs.bioexcel.eu/t/nvt-memory-error-for-free-energy-calculation/6100)
**Author:** [@luzgomez](https://gromacs.bioexcel.eu/u/luzgomez)\ **Replies:** 1\ **Last updated:** [April 4, 2023, 8:18am UTC](https://gromacs.bioexcel.eu/t/nvt-memory-error-for-free-energy-calculation/6100 "2023-04-04T08:18:18Z")
GROMACS version:2022.4 GROMACS modification: No Hi everyone, when I’m trying to make free energy calculations on NTV steps, but I got an memory error, and I don’t know what it means exactly, my box is 4nm side and it … --- ## [Users of spack-based GROMACS installations beware of possible performance loss!](https://gromacs.bioexcel.eu/t/users-of-spack-based-gromacs-installations-beware-of-possible-performance-loss/6077)
**Author:** [@pszilard](https://gromacs.bioexcel.eu/u/pszilard)\ **Replies:** 0\ **Last updated:** [March 30, 2023, 12:52pm UTC](https://gromacs.bioexcel.eu/t/users-of-spack-based-gromacs-installations-beware-of-possible-performance-loss/6077 "2023-03-30T12:52:37Z")
Hi, It has recently come to our attention default Spack builds of GROMACS use RelWithDebInfo instead of Release which is the default in our build system. Due to the lower optimization levels in RelWithDebInfo such build… --- ## [New blog on multi-GPU scalability](https://gromacs.bioexcel.eu/t/new-blog-on-multi-gpu-scalability/5779)
**Author:** [@alang](https://gromacs.bioexcel.eu/u/alang)\ **Replies:** 0\ **Last updated:** [February 10, 2023, 1:53pm UTC](https://gromacs.bioexcel.eu/t/new-blog-on-multi-gpu-scalability/5779 "2023-02-10T13:53:46Z")
GROMACS version: 2023 GROMACS modification: No Hi GROMACS users, Just a brief note to make you aware of a new blog article which highlights the new multi-GPU and multi-node capabilities in GROMACS 2023 (in particular … --- ## [GROMACS on Zen4: AVX2 vs AVX512](https://gromacs.bioexcel.eu/t/gromacs-on-zen4-avx2-vs-avx512/5720)
**Author:** [@pszilard](https://gromacs.bioexcel.eu/u/pszilard)\ **Replies:** 0\ **Last updated:** [February 3, 2023, 6:22pm UTC](https://gromacs.bioexcel.eu/t/gromacs-on-zen4-avx2-vs-avx512/5720 "2023-02-03T18:22:47Z")
Hi, Does anyone have experience with mdrun performance on Zen4 and specifically AVX2 vs AVX-512? Cheers, Szilárd --- ## [New blog post on maximizing GROMACS throughput on GPUs](https://gromacs.bioexcel.eu/t/new-blog-post-on-maximizing-gromacs-throughput-on-gpus/2944)
**Author:** [@alang](https://gromacs.bioexcel.eu/u/alang)\ **Replies:** 2\ **Last updated:** [January 13, 2023, 2:47pm UTC](https://gromacs.bioexcel.eu/t/new-blog-post-on-maximizing-gromacs-throughput-on-gpus/2944 "2023-01-13T14:47:38Z")
Dear GROMACS users, To address a frequently asked question, Szilárd Páll and I have just published a blog article that shows how to maximize GROMACS throughput on GPUs when running multiple simulations. It shows that, w… --- ## [Why load balancing is limited by minimum cell size in dimension X,Y,Z?](https://gromacs.bioexcel.eu/t/why-load-balancing-is-limited-by-minimum-cell-size-in-dimension-x-y-z/4738)
**Author:** [@gromacs\_amature](https://gromacs.bioexcel.eu/u/gromacs_amature)\ **Replies:** 1\ **Last updated:** [September 5, 2022, 11:20am UTC](https://gromacs.bioexcel.eu/t/why-load-balancing-is-limited-by-minimum-cell-size-in-dimension-x-y-z/4738 "2022-09-05T11:20:57Z")
GROMACS version: 5.1.4 i used this command for my ＭＤ simulation box set up gmx\_mpi editconf -f filename.pdb -o filename.pdb -d 1.2 after checking my log files, i noticed this error DD load balancing is limited by mi… --- ## [Regarding Editing the RAM and Compiling from GROMACS Source to improve performance](https://gromacs.bioexcel.eu/t/regarding-editing-the-ram-and-compiling-from-gromacs-source-to-improve-performance/4079)
**Author:** [@pssahoo](https://gromacs.bioexcel.eu/u/pssahoo)\ **Replies:** 0\ **Last updated:** [April 27, 2022, 5:01am UTC](https://gromacs.bioexcel.eu/t/regarding-editing-the-ram-and-compiling-from-gromacs-source-to-improve-performance/4079 "2022-04-27T05:01:40Z")
GROMACS version: 2021.3 GROMACS modification: Yes Here post your question Hi Where do I find the details of the CPU RAM which can be edited from current default limit of 16GB RAM to 32 GB RAM and then compile GROMACS a… --- ## [Reducing "Wait GPU state copy" for single GPU runs](https://gromacs.bioexcel.eu/t/reducing-wait-gpu-state-copy-for-single-gpu-runs/3555)
**Author:** [@hackettr](https://gromacs.bioexcel.eu/u/hackettr)\ **Replies:** 10\ **Last updated:** [February 4, 2022, 8:50am UTC](https://gromacs.bioexcel.eu/t/reducing-wait-gpu-state-copy-for-single-gpu-runs/3555 "2022-02-04T08:50:12Z")
GROMACS version: 2020.2-dev-20200430-5e78835-unkown GROMACS modification: https://catalog.ngc.nvidia.com/orgs/hpc/containers/gromacs I’m performing protein-bilayer simulations of ~360k atoms on a cluster running a dock… [Next page](https://gromacs.bioexcel.eu/tag/mdrun-performance/33.md?match_all_tags=true&page=1&tags%5B%5D=mdrun-performance)