[gmx-users] About Exclusion of bonded and non bonded parameters while running grompp
Justin A. Lemkul
jalemkul at vt.edu
Wed Jun 27 13:44:40 CEST 2012
On 6/27/12 7:36 AM, PAVAN PAYGHAN wrote:
> 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 ?
This output is perfectly normal, and is (or at least, should be) present for any
system that has more than monoatomic species.
> I really don't know why this screen output is coming which I never
> faced ? Is there any mistake by me ? Please suggest .
There is no mistake. Please refer to the manual, section 4.6.1.
> 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 .
> Pavan Payghan
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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