[gmx-users] Question about topologies
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???
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.
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users