[gmx-users] Forcefield question

Matthias Ernst Matthias.Ernst2 at student.kit.edu
Mon Feb 13 11:46:43 CET 2012


I am currently working with the AMBER forcefields provided by GROMACS. I 
noticed there are atoms in the forcefields (e.g. amber99 or amber03) 
with LJ parameters of 0.0 for sigma and epsilon. For example, the HO 
atom type is sometimes used (e.g. in SER or in the terminal Hs of DNA 
residues) but has such paramaters (see below).
I do not understand (yet) how that can give physically meaningful 
results. For sigma, I could understand that with combination rule 2, the 
resulting sigma for a bond is not zero. But the contribution to the 
total energy vanishes because of epsilon being zero and as such, I think 
clashes between such an atom and some other atom cannot be avoided 
because there is no energetic "penalty" for this.
Am I getting something wrong? Are there some default values that are 
applied if sigma and epsilon are zero or are those values stored 
somewhere else but not in ffnonbonded.itp?

Thank you for your help,

This is part of amber ffnonbonded.itp:

[ atomtypes ]
; name      at.num  mass     charge ptype  sigma      epsilon
Br          35      79.90    0.0000  A   0.00000e+00  0.00000e+00
HO           1       1.008   0.0000  A   0.00000e+00  0.00000e+00
HW           1       1.008   0.0000  A   0.00000e+00  0.00000e+00
FE          26      55.00    0.0000  A   0.00000e+00  0.00000e+00

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