[gmx-users] topology defaults directive

David L. Bostick dbostick at physics.unc.edu
Wed Oct 13 23:35:58 CEST 2004

Dear all,

In ffgmx.itp, the defaults directive confuses me. This file has the
following defaults:

[ defaults ]
; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
  1             1               no              1.0     1.0

This confuses me for 2 reasons:

1) The manual says that fudgeLJ and fudgeQQ are not
taken unless gen-pairs is yes. So, since in this case gen-pairs is no, does
this mean that fudgeLJ=fudgeQQ=1.0 doesn't really do anything?

2) I see that in ffgmxnb.itp [ pairtypes ] are listed for 1-4 LJ
interactions. So if in a molecule.itp file, I have

[ moleculetype ]
; Name   nrexcl
molecule     3

the 1-4 intramolecular LJ interactions will be given by the [ pairtypes ],
but what about the 1-4 coulomb interactions? With nrexcl = 3 and
gen-pairs=no, does this mean that the 1-4 coulomb interaction will be
completely excluded?


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