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
Gavin
parameter level
[defaults]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 3 yes 0.5 0.5
[atomtypes]
;type mass charge ptype sigma(nm) epsilon(kjmol-1)
;Molecular level
[moleculetype]
; name nrexcl
tertpentane 3
[atoms]
; atomnr type resnr residue name cgnr charge mass
[bonds]
; ai aj func b0(nm) kb(kjmol-1 nm-2)
[angles]
; ai aj ak func theta(deg) ktheta(kjmol-1 rad-2)
[dihedrals]
;System level
[system]
[molecules]
; moleculename number
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