[gmx-users] About Exclusion of bonded and non bonded parameters while running grompp
pavanapex at gmail.com
Wed Jun 27 13:36:17 CEST 2012
Dear Gromacs Users,
I am using gromacs version 4.5.5. , while running grompp (for any
purpose i.e. minimization , equilibration etc. )
I am getting following screen output without any warning, error or
note relevant to it.
"Generated 830 of the 2346 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_A'
Excluding 3 bonded neighbours molecule type 'Protein_B'
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 2 bonded neighbours molecule type 'SOL' "
My question is whether to ignore or consider this as an error ?
I really don't know why this screen output is coming which I never
faced ? Is there any mistake by me ? Please suggest .
cg.mdp for reference
; Conjugate Minimization
; Protein - Water - Ligand ( all free to move)
Title = Pro-Lig H2O
define = -DFLEXIBLE ; specifies flexible water
constraints = none
integrator = cg
nsteps = 2000
ns_type = grid
rlist = 1.2
coulombtype = pme
vdw-type = cut-off
rvdw = 1.2
rcoulomb = 1.2
; Energy Minimization Stuff
emtol = 0.0000001
emstep = 0.01
Thanking you in advance .
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