[gmx-users] About Exclusion of bonded and non bonded parameters while running grompp

[Justin A. Lemkul]

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.

-Justin

> 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 .
>
> Regards,
>
> Pavan Payghan
>

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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