Minimization and Production Errors - Bonds Rotated More than 30 Degrees

User discussions
1

GROMACS version:2020.1-Ubuntu-2020.1-1
GROMACS modification: No
Here post your question
I have persistent problems with errors of this type:

Step 3, time 0.006 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 136.755081, max 6260.414062 (between atoms 4759 and 4793)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length

In minimization and/or production runs for several molecules I am trying to model with lipidation of peptides. It seems to mainly affect alkyl chain C-H bonds.
In some runs, the forcefield parameters are unmodified from CHARMM-GUI, others I have edited myself using existing CHARMM forcefield parameters for PAM (palmitoyl lipid chains)

I have tried all sorts of things with the mdp files emstep, nsteps and many others from google searches, checking and regenerating coordinates (including previously minimized coordinates) many many times. I do not think there is a problem with the coordinates. I need to stop this bond rotation somehow.

2

I’m quite certain that it’s either the input coordinates or the force field that are the problem. It’s usually the coordinates. Have you checked atoms 4759 and 4793 and all atoms within, e.g., 0.2 nm (also across the periodic boundary, if the atoms are close to it)?