[gmx-users] [nonbond_params] section , choice of parameters

Amir Marcovitz amarcovitz at gmail.com
Wed Jul 28 11:38:58 CEST 2010

Hi All,

I want to exclude attractive Lennard-Jones interactions between atoms that i
defined in the ffamber99nb.itp file.
the properties of the dummy atom which I defined are:
*amber99_69    X      0.0000  0.0000  A   3.39967e-01  3.59824e-02*     ;
(i.e., Sigma=3.39967e-01 and Epsilon=3.59824e-02)

So , to exclude the attractive LJ term i added [nonbond_params] section as
*[ nonbond_params ]
; i j func c6 c12
  amber99_69     amber99_69      1      0.00000E-00     0.34252E-06*

(I set c6  to zero to eliminate the attractive LJ term..(or at least that is
what i was thinking)  )

I have a problem though: apparently from the simulation, *there is no
repulsion at all between the atoms*, as i see the atoms overlapping each
i guess that something is wrong with the choice of c12, not sure though.

the manual says (page 98), if I understand correctly:
C(12) = 4*Epsilon*Sigma^12         (hence,       *0.34252E-06 = 4* **
3.59824e-02*(** 3.39967e-01**)^12)

*can someone let me know how to fix this problem (i.e., just get rid of the
attractive terms according to the parameters above)?
 is the syntax i used for the nonbond_params OK?

Many Thanks,
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