<div dir="ltr">Hi All,<br><br>I want to exclude attractive Lennard-Jones interactions between atoms that i defined in the ffamber99nb.itp file.<br>the properties of the dummy atom which I defined are:<br><b>amber99_69 X 0.0000 0.0000 A 3.39967e-01 3.59824e-02</b> ; (i.e., Sigma=3.39967e-01 and Epsilon=3.59824e-02)<br>
<br>So , to exclude the attractive LJ term i added [nonbond_params] section as following:<br><b>[ nonbond_params ]<br>; i j func c6 c12<br> amber99_69 amber99_69 1 0.00000E-00 0.34252E-06</b><br><br>(I set c6 to zero to eliminate the attractive LJ term..(or at least that is what i was thinking) )<br>
<br>I have a problem though: apparently from the simulation, <u>there is no repulsion at all between the atoms</u>, as i see the atoms overlapping each other..<br>i guess that something is wrong with the choice of c12, not sure though.<br>
<br>the manual says (page 98), if I understand correctly: <br>C(12) = 4*Epsilon*Sigma^12 (hence, <b>0.34252E-06 = 4* </b><b>3.59824e-02*(</b><b> 3.39967e-01</b><b>)^12)<br><br></b>can someone let me know how to fix this problem (i.e., just get rid of the attractive terms according to the parameters above)?<br>
is the syntax i used for the nonbond_params OK? <br><br>Many Thanks,<br>amir<br></div>