[gmx-users] Non-attractive Lennard-Jones

[Dahlia Weiss]

I am running a simulation with only carbon (in the form of a 
hydrocarbon) and water in the OPLS-AA force field. I wanted to "turn 
off" the attractive part of the carbon-oxygen Lennard-Jones force, 
which I did by setting the C6 parameter of carbon to zero. I changed 
the combination rule to 1 and left the gen-pairs option as yes in the 
ffoplsaa.itp file. The results were not what I expected. I ran the same 
experiment in another force-field using different software and the 
results were more like what I would have expected. I therefore conclude 
that I did not succeed in turning off only the LJ carbon-oxygen 
attraction.

I obtained the c6 and c12 parameters through the equations:
c6(i) = epsilon(i)*sigma(i)^6
c12(i) = epsilon(i)*sigma(i)^12
Perhaps this is the problem?


Below are the files that I changed.

ffoplsaa_hs.itp
-------------------

#define _FF_OPLS
#define _FF_OPLSAA

[ defaults ]
; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
1               1               yes             0.5     0.5

#include "ffoplsaanb_hs.itp"
#include "ffoplsaabon_hs.itp"


ffoplsaanb_hs.itp
-----------------
[ atomtypes ]
;name  bond_type    mass    charge   ptype      c6           c12

opls_501   CB     12.01100   0.000       A   0.00000E+00   4.69340E-06
opls_116   OW     15.99940   0.000       A   2.60000E-03   2.63350E-06
opls_117   HW      1.00800   0.000       A   0.00000E+00   0.00000E+00


ffoplsaabon_hs.itp
------------------
[ bondtypes ]
   ; i    j func        b0          kb
    OW   HW    1   0.09572    502080.0
    CB   CB    1   0.13900    502080.0


[ angletypes ]
   ; i    j    k func       tHC         cth
    CB   CB   CB    1   120.000     418.400
    HW   OW   HW    1   109.500     502.080


[ dihedraltypes ]
;  i    j    k    l   func     coefficients
   X      CB     CB     X       3     30.33400   0.00000 -30.33400 
0.00000   0.00000   0.00000 ; aromatic ring


Thank you,
Dahlia Weiss