[gmx-users] non-bonding parameters

Gavin Melaugh gmelaugh01 at qub.ac.uk
Tue Sep 28 16:03:02 CEST 2010

Hi all

I need some clarification on a few matters please. I have always used topology files (for one molecule) with the following format (below with values excluded). 
Does the format below enable LJ energies to be calculated?
Does it enable 1,4 interactions to be calculated? (In reference to gen-pair = yes.) Do I need a pair list or the following directives [nonbond_params] and [pairtypes]. I have always assumed that all LJ interactions both bonded 1,4 and non-bonded would be calculated from the parameters in the atomtypes directive using the corresponding comb rule.

Many Thanks 


parameter level
; nbfunc    comb-rule     gen-pairs        fudgeLJ     fudgeQQ
     1         3              yes            0.5         0.5

;type     mass           charge      ptype     sigma(nm)     epsilon(kjmol-1)

;Molecular level
;       name         nrexcl
        tertpentane      3

; atomnr  type   resnr  residue   name    cgnr     charge     mass

;  ai    aj   func   b0(nm)       kb(kjmol-1 nm-2)

;  ai    aj    ak   func  theta(deg)    ktheta(kjmol-1 rad-2)


;System level

; moleculename     number

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