# \#replica-exchange **URL:** https://gromacs.bioexcel.eu/tag/replica-exchange/37.md [Latest](https://gromacs.bioexcel.eu/latest.md) · [Categories](https://gromacs.bioexcel.eu/categories.md) · [Tags](https://gromacs.bioexcel.eu/tags.md) --- ## [Sbatch: error: Batch job submission failed: Node count specification invalid](https://gromacs.bioexcel.eu/t/sbatch-error-batch-job-submission-failed-node-count-specification-invalid/12322)
**Author:** [@FedeAll](https://gromacs.bioexcel.eu/u/FedeAll)\ **Replies:** 2\ **Last updated:** [July 4, 2025, 10:00am UTC](https://gromacs.bioexcel.eu/t/sbatch-error-batch-job-submission-failed-node-count-specification-invalid/12322 "2025-07-04T10:00:47Z")
GROMACS version: 2021.7 GROMACS modification: Hi everyone! I have this script: #!/bin/bash #SBATCH -N76 #SBATCH --ntasks-per-node=4 #SBATCH --cpus-per-task=8 #SBATCH --time=24:00:00 #SBATCH --gres=gpu:4 #SBATCH … --- ## [Segmentation fault with REMD+GPU--potential bug?](https://gromacs.bioexcel.eu/t/segmentation-fault-with-remd-gpu-potential-bug/11807)
**Author:** [@ianbongalonta](https://gromacs.bioexcel.eu/u/ianbongalonta)\ **Replies:** 5\ **Last updated:** [April 11, 2025, 1:46pm UTC](https://gromacs.bioexcel.eu/t/segmentation-fault-with-remd-gpu-potential-bug/11807 "2025-04-11T13:46:02Z")
GROMACS version: gromacs/2024.1+oneapi-2023.1 GROMACS modification: No Hi everyone, I am currently running a replica exchange simulation on a 30-mer of the PNIPAM polymer, with a modified OPLS-AA and SPCE water (from … --- ## [Correct Setup for Temperature Replica Exchange (T-REMD) in GROMACS Without PLUMED](https://gromacs.bioexcel.eu/t/correct-setup-for-temperature-replica-exchange-t-remd-in-gromacs-without-plumed/11563)
**Author:** [@b-omics](https://gromacs.bioexcel.eu/u/b-omics)\ **Replies:** 1\ **Last updated:** [February 19, 2025, 1:52pm UTC](https://gromacs.bioexcel.eu/t/correct-setup-for-temperature-replica-exchange-t-remd-in-gromacs-without-plumed/11563 "2025-02-19T13:52:17Z")
GROMACS version: 2024.4 GROMACS modification: Yes/No Here post your question I have a question regarding temperature replica exchange (T-REMD) in GROMACS (without using PLUMED). After completing energy minimization, … --- ## [Encountered crashed mdrun when request 2 GPUs on parallel simulations with 15 replicas](https://gromacs.bioexcel.eu/t/encountered-crashed-mdrun-when-request-2-gpus-on-parallel-simulations-with-15-replicas/10560)
**Author:** [@MinhGromacs123](https://gromacs.bioexcel.eu/u/MinhGromacs123)\ **Replies:** 0\ **Last updated:** [November 15, 2024, 5:28pm UTC](https://gromacs.bioexcel.eu/t/encountered-crashed-mdrun-when-request-2-gpus-on-parallel-simulations-with-15-replicas/10560 "2024-11-15T17:28:56Z")
GROMACS version: 2023 GROMACS modification: No Here post your question: I have a gromacs built 2023 and plumed version 2.9.0 to do bias-exchange metadynamics (BE-META) simulation for a system with 15 replicas. When I … --- ## [My REMD it is giving me 0.0 of probability](https://gromacs.bioexcel.eu/t/my-remd-it-is-giving-me-0-0-of-probability/10178)
**Author:** [@jorge\_leon](https://gromacs.bioexcel.eu/u/jorge_leon)\ **Replies:** 4\ **Last updated:** [September 24, 2024, 5:13am UTC](https://gromacs.bioexcel.eu/t/my-remd-it-is-giving-me-0-0-of-probability/10178 "2024-09-24T05:13:56Z")
GROMACS version:2023 GROMACS modification: No Hello everyone, I’m running a replica exchange simulation without PLUMED and could use some guidance. Here’s the command I’m using: srun -n SLURM\_NTASKS gmx\_mpi mdrun -de… --- ## [No swap in replica exchange](https://gromacs.bioexcel.eu/t/no-swap-in-replica-exchange/10206)
**Author:** [@jorge\_leon](https://gromacs.bioexcel.eu/u/jorge_leon)\ **Replies:** 0\ **Last updated:** [September 21, 2024, 5:42pm UTC](https://gromacs.bioexcel.eu/t/no-swap-in-replica-exchange/10206 "2024-09-21T17:42:47Z")
GROMACS version: GROMACS modification: Yes/No Here post your question : I’m not having swap in my replica exchange simulation. Does anybody can give an advice? --- ## [T-REMD simulations result in 5x performance](https://gromacs.bioexcel.eu/t/t-remd-simulations-result-in-5x-performance/8992)
**Author:** [@tlfobe](https://gromacs.bioexcel.eu/u/tlfobe)\ **Replies:** 2\ **Last updated:** [June 2, 2024, 10:30am UTC](https://gromacs.bioexcel.eu/t/t-remd-simulations-result-in-5x-performance/8992 "2024-06-02T10:30:59Z")
GROMACS version: 2023.4 GROMACS modification: No Hello Gromacs forum members! I’m working on some T-REMD simulations of an enzyme where I am using enhance sampling to sample different settled configurations of the act… --- ## [Metadynamics simulation unable to be restarted from checkpoint, despite mdrun maxh flag used](https://gromacs.bioexcel.eu/t/metadynamics-simulation-unable-to-be-restarted-from-checkpoint-despite-mdrun-maxh-flag-used/8023)
**Author:** [@oriol-barcenas](https://gromacs.bioexcel.eu/u/oriol-barcenas)\ **Replies:** 1\ **Last updated:** [April 11, 2024, 11:21am UTC](https://gromacs.bioexcel.eu/t/metadynamics-simulation-unable-to-be-restarted-from-checkpoint-despite-mdrun-maxh-flag-used/8023 "2024-04-11T11:21:37Z")
GROMACS version: 2020.4-MODIFIED This program has been built from source code that has been altered and does not match the code released as part of the official GROMACS version 2020.4-MODIFIED. If you did not intend t… --- ## [REMD with GROMACS2023\_par](https://gromacs.bioexcel.eu/t/remd-with-gromacs2023-par/8648)
**Author:** [@valerio](https://gromacs.bioexcel.eu/u/valerio)\ **Replies:** 0\ **Last updated:** [March 19, 2024, 2:00pm UTC](https://gromacs.bioexcel.eu/t/remd-with-gromacs2023-par/8648 "2024-03-19T14:00:24Z")
GROMACS version:2023 GROMACS modification: Yes Greetings to you all I have run a REMD simulation with the following details: dodecahedral box with -d 1 spacing 14 temperatures each one run for 10 ns. System equilibr… --- ## [How to run replica exchage simulation in GROMACS](https://gromacs.bioexcel.eu/t/how-to-run-replica-exchage-simulation-in-gromacs/8012)
**Author:** [@JianjunTAO](https://gromacs.bioexcel.eu/u/JianjunTAO)\ **Replies:** 0\ **Last updated:** [January 9, 2024, 2:10pm UTC](https://gromacs.bioexcel.eu/t/how-to-run-replica-exchage-simulation-in-gromacs/8012 "2024-01-09T14:10:03Z")
GROMACS version: GROMACS modification: Yes/No Here post your question Hey, I have been wanting to perform Replica Exchange MD (REMD), but I found 0 tutorial and functioning temperature distribution server. Could some… --- ## [How to run replica exchange with NVIDIA MPS/MIG](https://gromacs.bioexcel.eu/t/how-to-run-replica-exchange-with-nvidia-mps-mig/7139)
**Author:** [@roozi](https://gromacs.bioexcel.eu/u/roozi)\ **Replies:** 3\ **Last updated:** [September 11, 2023, 9:44am UTC](https://gromacs.bioexcel.eu/t/how-to-run-replica-exchange-with-nvidia-mps-mig/7139 "2023-09-11T09:44:55Z")
GROMACS version:2023 GROMACS modification: No Hi, Just came upon below link while trying to find tricks to increase output of a REMD run on gmx using a GPU based HPC server: https://developer.nvidia.com/blog/maximizi… --- ## [MDRUN crash during gREST simulation under NVT ensemble](https://gromacs.bioexcel.eu/t/mdrun-crash-during-grest-simulation-under-nvt-ensemble/6535)
**Author:** [@jimmy\_chang](https://gromacs.bioexcel.eu/u/jimmy_chang)\ **Replies:** 1\ **Last updated:** [June 26, 2023, 4:21pm UTC](https://gromacs.bioexcel.eu/t/mdrun-crash-during-grest-simulation-under-nvt-ensemble/6535 "2023-06-26T16:21:29Z")
GROMACS version: 2022.3 GROMACS modification: No Hello everyone. I am currently using GROMACS ver. 2022.3 patched with PLUMED ver. 2.8.1., and I’ve been trying to replicate the gREST simulations from Oshima et al. (J.… --- ## [Remd.mdp file not being read properly](https://gromacs.bioexcel.eu/t/remd-mdp-file-not-being-read-properly/6431)
**Author:** [@ksr](https://gromacs.bioexcel.eu/u/ksr)\ **Replies:** 0\ **Last updated:** [May 17, 2023, 9:55pm UTC](https://gromacs.bioexcel.eu/t/remd-mdp-file-not-being-read-properly/6431 "2023-05-17T21:55:20Z")
GROMACS version:2023 GROMACS modification: No I’m doing something dumb. My remd.mdp file contains these entries: ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostati… --- ## [Native Implementation of REST2](https://gromacs.bioexcel.eu/t/native-implementation-of-rest2/6013)
**Author:** [@Dan](https://gromacs.bioexcel.eu/u/Dan)\ **Replies:** 4\ **Last updated:** [March 22, 2023, 2:48pm UTC](https://gromacs.bioexcel.eu/t/native-implementation-of-rest2/6013 "2023-03-22T14:48:29Z")
Hello, Do I just need to set the protein molecule in couple-moltype and apply lambdas to run a REST2? Along with expanded ensemble options? Thank you, Dan --- ## [REMD restart](https://gromacs.bioexcel.eu/t/remd-restart/4748)
**Author:** [@siddharths](https://gromacs.bioexcel.eu/u/siddharths)\ **Replies:** 1\ **Last updated:** [September 14, 2022, 1:42pm UTC](https://gromacs.bioexcel.eu/t/remd-restart/4748 "2022-09-14T13:42:32Z")
GROMACS version: gmx\_mpi version 2020 GROMACS modification: Yes/No Here post your question Hello everyone, I am running 8 replica system for 1000 ns and I need to restart my simulations- here is my code for running i… --- ## [Using gromacs 2022 to run N replicas on ONE gpu](https://gromacs.bioexcel.eu/t/using-gromacs-2022-to-run-n-replicas-on-one-gpu/4357)
**Author:** [@aweigle2](https://gromacs.bioexcel.eu/u/aweigle2)\ **Replies:** 0\ **Last updated:** [June 24, 2022, 2:57pm UTC](https://gromacs.bioexcel.eu/t/using-gromacs-2022-to-run-n-replicas-on-one-gpu/4357 "2022-06-24T14:57:29Z")
GROMACS version: 2022.2 (CUDA, MPI) GROMACS modification: No CUDA driver: 11.70 CUDA runtime: 11.60 Hello Gromacs Forum, I am new to gromacs but would like to run temperature replica exchange. I am also new to repli… --- ## [Extraction of trajectory for multimeric system](https://gromacs.bioexcel.eu/t/extraction-of-trajectory-for-multimeric-system/3842)
**Author:** [@priyanka](https://gromacs.bioexcel.eu/u/priyanka)\ **Replies:** 9\ **Last updated:** [April 8, 2022, 5:38am UTC](https://gromacs.bioexcel.eu/t/extraction-of-trajectory-for-multimeric-system/3842 "2022-04-08T05:38:25Z")
GROMACS version:5.1.6 Question: I have run a REMD simulation for a dimer and I concatenated the trajectory of all. This dimer during the simulation got separated in the middle to individual monomers and again forms dim… --- ## [High-temperature MD simulations blow up after switching from GROMACS 5.0.2 to 2021.2](https://gromacs.bioexcel.eu/t/high-temperature-md-simulations-blow-up-after-switching-from-gromacs-5-0-2-to-2021-2/3846)
**Author:** [@astelmakh](https://gromacs.bioexcel.eu/u/astelmakh)\ **Replies:** 1\ **Last updated:** [March 21, 2022, 10:23am UTC](https://gromacs.bioexcel.eu/t/high-temperature-md-simulations-blow-up-after-switching-from-gromacs-5-0-2-to-2021-2/3846 "2022-03-21T10:23:17Z")
GROMACS version: 5.0.2 and 2021.2 GROMACS modification: No I am studying adsorbtion of organic surfactants onto the surface of inorganic crystal using replica-exchange simulations in NVT ensemble (replicas between 300 … --- ## [What are the accepted values for the exchange probability of REMD simulation?](https://gromacs.bioexcel.eu/t/what-are-the-accepted-values-for-the-exchange-probability-of-remd-simulation/3469)
**Author:** [@sam](https://gromacs.bioexcel.eu/u/sam)\ **Replies:** 9\ **Last updated:** [January 28, 2022, 6:48pm UTC](https://gromacs.bioexcel.eu/t/what-are-the-accepted-values-for-the-exchange-probability-of-remd-simulation/3469 "2022-01-28T18:48:25Z")
I tried more than one time and got these values, how can I know whether values are accepted or not for the exchange probability of REMD simulation ?