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GROMACS 2024+ GPU runs require explicit -ntmpi; OMP_NUM_THREADS leakage breaks resume on Slurm. Proposal: scope OMP env per-run and set sane defaults in Mdrun

Status: Open.

#30 In bioexcel/biobb_gromacs;

· hariseldon99 opened on Oct 16, 2025

Point biobb to a manually compiled version of Gromacs

Status: Open.

#23 In bioexcel/biobb_gromacs;

· JSLJ23 opened on Sep 5, 2024

new grompp/mdrun behaviour conflicts with .cpt file?

stale

Status: Open.

#3 In bioexcel/biobb_gromacs;

· pgbarletta opened on Feb 2, 2023

Change pre-configured mdp files

stale

Status: Open.

#7 In bioexcel/biobb_gromacs;

· adamhospital opened on Jul 1, 2022

Default mdp files from the official gromacs tutorials

stale

Status: Open.

#9 In bioexcel/biobb_gromacs;

· adamhospital opened on Jun 15, 2022

Solvate create new selection property for the solvent

stale

Status: Open.

#12 In bioexcel/biobb_gromacs;

· PauAndrio opened on Apr 23, 2021

genrestr bb, possibility to add the new position restraint file in the topology (avoiding overwrite)

stale

Status: Open.

#13 In bioexcel/biobb_gromacs;

· adamhospital opened on Dec 23, 2020

gmx genion input ndx + enable group selection

stale

Status: Open.

#14 In bioexcel/biobb_gromacs;

· adamhospital opened on Dec 23, 2020

gmx select, append new generated group to input ndx

stale

Status: Open.

#15 In bioexcel/biobb_gromacs;

· adamhospital opened on Dec 23, 2020

gmxselect biobb does not pass docker test

stale

Status: Open.

#17 In bioexcel/biobb_gromacs;

· PauAndrio opened on Dec 20, 2020

New tool: gromacs_extra.GenerateMDP a Biobb to generate MDP files.

stale

Status: Open.

#18 In bioexcel/biobb_gromacs;

· PauAndrio opened on Dec 20, 2020

New tool: gmx insert-molecules

stale

Status: Open.

#19 In bioexcel/biobb_gromacs;

· adamhospital opened on Jun 5, 2020