[gmx-users] a question related to grompp command

[Peter C. Lai]

On 2012-09-29 12:42:29AM -0700, Acoot Brett wrote:
> 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.

Turning refers to turning bonds into constraints are defined in the .mdp file:

constraints = whatever you have defined here (probably all-bonds if grompp
is reporting that all bonds are turned into constraints)

neighbor exclusions are from the beginning of the topology file for that 
particular [ moleculetype ] in the nrexcl field

[ moleculetype ]
; name	nrexcl
Protein_chain_A	3

nonbonded interactions between atoms that are no further than nrexcl bonds 
away are excluded. See also
http://lists.gromacs.org/pipermail/gmx-users/2011-May/061072.html

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