[gmx-users] Non-attractive Lennard-Jones

[David]

On Wed, 2005-04-27 at 12:09 -0700, Dahlia Weiss wrote:
> The LJ matrix looks correct according to the parameters that I put in.
>              functype[0]=LJ_SR, c6= 0.00000000e+00, c12= 3.37400002e-06
>              functype[1]=LJ_SR, c6= 0.00000000e+00, c12= 2.98061718e-06
>              functype[2]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
>              functype[3]=LJ_SR, c6= 0.00000000e+00, c12= 2.98061718e-06
>              functype[4]=LJ_SR, c6= 2.61710002e-03, c12= 2.63309994e-06
>              functype[5]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
>              functype[6]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
>              functype[7]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
>              functype[8]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
> 
> When I looked at other force fields, for example at ffgmxnb.itp, the C6  
> and C12 parameters look the same as what I gave. However, the  
> interaction parameter between carbon and oxygen is completely  
> different.
> 
> ffgmxnb.itp
> --------------
> [ atomtypes ]
> ;name    mass    charge   ptype      c6           c12
>     OW    15.99940       0.000       A   0.26171E-02   0.26331E-05
>     CB    12.01100       0.000       A   0.23402E-02   0.33740E-05
> 
> [ nonbond_params ]
>    ; i    j func          c6           c12
>     OW   CB    1 0.24748E-02   0.15818E-05
>     CB   CB    1 0.23402E-02   0.33740E-05
>     OW   OW    1 0.26171E-02   0.26331E-05
> 
> As you can see in ffgmxnb.itp  c12(OW   CB) does not equal  
> (c12(OW)*c12(CB) )^ 1/2, which is what I thought. Is this because of  
> some difference between the GMX and OPLS force-field? Or is this some  
> problem in my simulation?
No this is by design of the force field.

> 
> It looks like the repulsive term in my simulation is too strong. Is it  
> possible to set the non-bond params in the OPLS force-field? I tried  
> pasting the [ nonbond_params ] section into my ffoplsaanb.itp file, but  
> this didn't work.
Since OPLS is implemented as sigma/epsilon it is not trivial to make C6
zero.



-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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