[gmx-users] Question about topologies

Thanasis Koukoulas koukoulas_th at yahoo.gr
Fri Jun 18 11:54:27 CEST 2010

[ atomtypes ];   type      mass    charge    ptype       c6            c12    CH3     15.035     0.000    A       9.0638e-3      2.5206e-5    CH2     14.027     0.000    A       5.8108e-3      2.2071e-5    CS2     14.027     0.000    A       5.8108e-3      2.2071e-5    OS      15.999     0.000    A       8.8147e-4      4.2477e-7     OA      15.999     0.000    A       2.3465e-3      1.7802e-6    HO       1.008     0.000    A       0.0000e00      0.0000e00 
at atomtypes i can give c6 and c12 values and gromacs will generate the c6ij and c12ij values from the formulas i have chosen with selecting combination rule Am i right????
in my case i gave c6 and c12 as c6i=4*ei*σi^6 and c12i=4*ei*σi^12 and i chose combination rule 1. so gromacs will generate the c6ij and c12ij as c6ij=sqrt(C6iC6j) and c12ij=sqrt(c6i*c12j)
So if in my topology I put [nonbond_params] what happens then? the values from [nonbond_params] c6 and c12 are being replaced by the values gromacs finds from the equations???
for example
if i have 
CH3 CH3 5e-3 6e-5
and gromacs calculates from the [atomtypes] are different lets say (i didnt do the calculation it is an assumption  value) 3e-2 and 3e-5 which values gromacs accepts?i have read the manual but it isnd clear how this works. 
please someone enlighten me.

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