Position restraints causing mdrun to stall on step 0

User discussions
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1

GROMACS version: 2024.4
GROMACS modification: No

Hi all,

I’m having issues with Gromacs 2024.4. I’m running a membrane simulation with antimicrobial peptides. Our group typically uses a layer of frozen water beneath the membrane- this stops any stray peptides that cross the pbc from interfering with the inner membrane leaflet. I have no troubles equilibrating with a 10fs timestep, but once I try a 20fs timestep, mdrun immediately stalls at step 0 and will not progress any further.

I am confident it is an issue with the frozen water layer, which has strong position restraints on it. Any ideas on why the larger timestep could be causing my issue?

2

The maximum time step in atomistic MD simulations is 2 or 2.5 fs (unless you use some tricks). Any simulation will crash when using a 10 fs time step.

3

I should have mentioned- this is a coarse grain system!

4

Then I have no clue. I suppose it’s Martini. Better ask there.