[gmx-users] Setting the C6 LJ term for OPLSA FF

[Mark Abraham]

On 4/04/2011 6:55 PM, Luca Bellucci wrote:
> Dear all
> I need to change sigma and epsilon for non-bonded parameters of the OPLSA FF.
> In particular I want to set the attractive part of the LJ potential to zero
> (C6=0).
> In doing this I have read the manual but unfortunately the reported
> explanation did not help me. To understand how it works in a reliable way,
> I followed the Berk suggestions available at
> http://lists.gromacs.org/pipermail/gmx-users/2010-December/056303.html
> and i decided to report a simple example.
>
> The main rules are in forcefield.itp file and for OPLSA FF they are:
>   ; nbfunc   comb-rule   gen-pairs     fudgeLJ     fudgeQQ
>       1               3                  yes                   0.5        0.5
>
> The non-bonded force field parameters for two atoms are in ffnonbonded.itp
> file and they look like:
>
> [ atomtypes ]
> ; name   bond_type  mass       charge  ptype    sigma       epsilon
>   opls_1   C     6        12.01100   0.500        A       sig_1        esp_1
>   opls_2   O     8       15.99940   -0.500       A       sig_2        eps_2
>
>  From these values I am going to define the non-bonded parameter between a
> couple of atoms as:
>
> [ nonbond_params ]
>    i      j     func              SIG_ij                  EPS_ij
> opls_1 opls_2  1    (sig_1*sig2)^1/2  (eps_1*eps_2)^1/2 ; Normal behavior
>
> However, if I want the attractive term C6 of LJ potential equal zero, I should
> set sig_12=-sig_12
>
> [ nonbond_params ]
>    i      j     func                SIG_ij                 EPS_ij
> opls_1 opls_2  1   -(sig_1*sig_2)^1/2  (eps_1*eps_2)^1/2  ; -sig_ij ->  C6=0
>
> It is right?

Yes, I think so. Set up a two-atom example to compare the normal and 
modified functions. Get a trajectory frame, make energy group(s) 
containing only pair(s) of atoms of interest and use mdrun -rerun to 
compute the energy to your heart's content.

Mark