[gmx-users] non-bonded parameters

David van der Spoel spoel at xray.bmc.uu.se
Thu Nov 17 09:13:41 CET 2005

On Thu, 2005-11-17 at 07:40 +0000, nk yx wrote:
> hi all,
>     I am confused about the calculation of non-bonded LJ parameters in the 
> ffG43a1nb.itp. According to the manual, the combination rule of C6 and C12 
> is:
> Cij(6)=(Cii(6)*Cjj(6))^0.5
> Cij(12)=(Cii(12)*Cjj(12))^0.5
> However,in the ffG43a1nb.itp file, the values seem not to be in agreement 
> with the rule. For example,
> O  C6=0.0022619536 C12=7.4149321e-07
> OM C6=0.0022619536 C12=7.4149321e-07
> OA C6=0.0022619536 C12=1.505529e-06
> According to the rule, 
> O OA   C6=0.0022619536 
>        C12=(7.4149321e-07 * 1.505529e-06)^0.5 = 1.0565697e-06 
> but the value is 1.380375e-06 in the ffG43a1nb.itp.
> In addition, C12 value between O and OM, and tween O and OA should be the 
> same, but in the file, C12 is 1.38380375e-06 and 2.258907e-06,respectively.
> Could anybody tell me why? Thanks in advance.
This is an oddity of the gromos force field. It doesn't work completely
with combination rules. The numbers are correct though. For more info
you will need to look up gromos documentation.
> Regards,
> nkyx
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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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