[gmx-users] Non-attractive Lennard-Jones

[David van der Spoel]

On Mon, 2005-04-25 at 14:24 -0700, Dahlia Weiss wrote:
> 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?

Not necessarily. Checkt your tpr file before use with the gmxdump
utility to see what the parameters look like. Do
gmxdump -s topol.tpr | less
and search for idef (interaction definition). There you'll find the LJ
matrix.

> 
> 
> 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
> 
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-- 
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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