Dear all,
I’m using the standard workflow for preparing a PSM lipid bilayer as suggested in the Martini 3 tutorials. I successfully generated the membrane.gro file using insane.py and proceeded to energy minimization using the following commands:
gmx grompp -f martini_v2.x_new-rf-em.mdp -c membrane.gro -p topol.top -o psm.tpr
gmx mdrun -s psm.tpr -v -c minimized.gro
I’m using the martini_v2.x_new-rf-em.mdp file provided in the M3-Lipid-Parameters/openbeta at main · Martini-Force-Field-Initiative/M3-Lipid-Parameters · GitHub
However, during the minimization step, I encountered a large number of LINCS warnings, and the minimization was not completed successfully.
**Program: gmx mdrun, version 2021.4-Ubuntu-2021.4-2
Source file: src/gromacs/mdlib/constr.cpp (line 241)
Fatal error:
Too many LINCS warnings (1463)
If you know what you are doing you can adjust the lincs warning threshold in
your mdp file
or set the environment variable GMX_MAXCONSTRWARN to -1,
but normally it is better to fix the problem.**
Has anyone experienced similar issues, or is there something I might be overlooking in the setup?
Any help or suggestions would be greatly appreciated.
Best regards,
Ishwar