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 following: *[ 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 other.. 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, amir
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