@hess : Perfect, then I will leave the values as they are!
@MagnusL : This is a mdp file or a protein (GPCR) in membrane system. The system is around 100k atoms big. I generated the system using CHARMM-GUI (AMBER force field / GROMACS input files). By default, CHARMM-GUI creates 3 temperature coupling groups (SOLU, SOLV, MEMB). When I modified the mdp file I just went with it. Would there be any benefit using just 2 groups (SOLV, SOLU_MEMB)?
Just as a follow up question - when I grompp’d a mdp file with
mass-repartition-factor = 3
to generate a trp file I received following note:
NOTE 1 [file topol.top, line 28]:
The bond in molecule-type MOL between atoms 30 O4 and 39 C10 has an
estimated oscillational period of 2.1e-02 ps, which is less than 10 times
the time step of 4.0e-03 ps.
Maybe you forgot to change the constraints mdp option.
During the simulations I receive following warning:
Step 8151, time 32.604 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000118, max 0.005614 (between atoms 6511 and 6513)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
6511 6514 30.7 0.1091 0.1084 0.1090
I did some research and noticed that other users experience similar problems:
Is there any solution to it? I use the AMBER force field and from my understanding I can only constrain the bonds to hydrogen atoms (constraints = h-bonds). So, using (constraints = all-bonds) would not be an option since the force field was designed for that.