[gmx-users] a question related to grompp command

[Acoot Brett]

Dear All,

I just run a grompp command "grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr". It gives the following message,

Generated 2211 of the 2211 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2211 of the 2211 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
turning all bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
turning all bonds into constraints...
Excluding 1 bonded neighbours molecule type 'NA'
turning all bonds into constraints...
Excluding 1 bonded neighbours molecule type 'CL'

Will you please tell me why grompp "exclude" and "turning"? What are their functions? Based on what grompp process "exclude" and "turning"?

I am looking forward to getting your reply.

Cheers,

Acoot