[gmx-users] atom types

[Gavin Melaugh]

Hi all

A very quick question. I have an atom-type labelled CH in the atom-types
with a particular charge, and in the atom list I assign some of these
specific atoms with zero charge as below. When I generate 1,4
interactions using gen_pairs =yes, what charge for the CH type does it
use? Does gromacs assign the CH with the different charge as a new atom
type.

;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)
   CB     12.011000      0.000000       A      0.355000      0.292880
   CA     12.011000     -0.115000       A      0.355000      0.292880
   HC      1.008000      0.115000       A      0.242000      0.125520
   CU     13.019000      0.265000       A      0.350000      0.334720
   NU     14.007000     -0.597000       A      0.325000      0.711280
   CH     13.019000      0.332000       A      0.385000      0.334720
   C3     15.035000      0.000000       A      0.391000      0.669440
   C2     14.027000      0.000000       A      0.390500      0.493712

;Molecular level
[moleculetype]
;       name         nrexcl
        isotridecylcage      3

[atoms]
.................
 72      CH       1   CGE        CH      24      0.3320     13.0190
   73      C2       1   CGE        C2      25      0.0000     14.0270
   74      C2       1   CGE        C2      25      0.0000     14.0270
   75      C2       1   CGE        C2      25      0.0000     14.0270
   76      C2       1   CGE        C2      26      0.0000     14.0270
   77      C2       1   CGE        C2      26      0.0000     14.0270
   78      C2       1   CGE        C2      26      0.0000     14.0270
   79      C2       1   CGE        C2      27      0.0000     14.0270
   80      C2       1   CGE        C2      27      0.0000     14.0270
   81      C2       1   CGE        C2      27      0.0000     14.0270
   82      C2       1   CGE        C2      28      0.0000     14.0270
   83      CH       1   CGE        CH      28      0.0000     13.0190
   84      C3       1   CGE        C3      29      0.0000     15.0350


Many Thanks

Gavin