https://github.com/tylerjereddy/gmx_martini3_alchembed_repro

https://github.com/tylerjereddy/gmx_martini3_alchembed_repro

Last synced: 9 days ago
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• Host: GitHub
• URL: https://github.com/tylerjereddy/gmx_martini3_alchembed_repro
• Owner: tylerjereddy
• Created: 2024-09-10T17:40:14.000Z (4 months ago)
• Default Branch: main
• Last Pushed: 2024-09-10T17:40:32.000Z (4 months ago)
• Last Synced: 2024-10-31T05:42:45.448Z (2 months ago)
• Size: 1.27 MB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
GROMACS 2024.2 MARTINI 3 Alchembed (lambda scaling) reproducer

The problem appears to the forcefield for the MARTINI 3 lipid POPI. Steps,

using GROMACS 2024.2 with this repo:

- `gmx grompp -f alchembed-cg.mdp -c system.gro -p topology.top -o alchembed.tpr -maxwarn 20`

- `gmx mdrun -v -s alchembed.tpr -deffnm alchembed_1x_lipids -nt 1 -ntmpi 1`

which should crash/reproduce:

```

Program:     gmx mdrun, version 2024.2

Source file: src/gromacs/topology/topsort.cpp (line 142)

Fatal error:

Function type Restr. Angles does not currently support being perturbed in free

energy calculations

```