[gmx-users] Lincs warning in free energy calculation (FAISAL NABI)

[Sadaf Rani]

Dear Gromacs users
I am using amber99sb-ildn.ff force field for protein and I used GAFF for
ligand parameterization.
I tried different options e.g using constraint =all bonds as well as
h-bonds. Reducing the time step to 1 fs but still, I could not solve the
problem and get lincs warning production run as below:-
Step 106202, time 212.404 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.035343, max 2.112628 (between atoms 3770 and 3773)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   3437   3438   90.0    2.2392   0.1552      0.1080
   3770   3771   90.0    0.1045   0.1696      0.1090
   3770   3772   90.0    2.9369   0.1212      0.1090
   3770   3773   90.0    0.1043   0.3393      0.1090
Wrote pdb files with previous and current coordinates

Step 106202, time 212.404 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.035038, max 2.096736 (between atoms 3770 and 3773)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   3437   3438   90.0    2.2392   0.1540      0.1080
   3770   3771   90.0    0.1045   0.1689      0.1090
   3770   3772   90.0    2.9369   0.1198      0.1090
   3770   3773   90.0    0.1043   0.3375      0.1090

I would really appreciate your help in fixing this problem I am
facing since long.

Thanks.

Sadaf