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I am trying to run a production run with constraints all bonds using constraints algorithm. Since during equilibration I tried to run at higher time step 20fs Coarse grained simulation I got this warning WARNING 1 [file dex.top, line 15]:
The bond in molecule-type Protein between atoms 7 SC1 and 8 SC2 has an
estimated oscillational period of 2.7e-02 ps, which is less than 5 times
the time step of 2.0e-02 ps.
Maybe you forgot to change the constraints mdp option.
so I tried to use constraints I got the same error as in equilibration.
Fatal error:
A constraint is connected to 33 constraints, this is more than the 31 allowed
for constraints participating in triangles