[gmx-users] ffG43a1nb.itp matrix

[David van der Spoel]

Magnus Andersson wrote:
> Hi,
> 
> I've found som C6 & C12 LJ parameters that I want to add for iodine. In
> the file ffG43a1nb.itp I think it should be possible to just add the
> parameters for iodine in the upper part and then somehow generate new
> parameters for the possible interactions, ie lower part of file.
> 
> How is this done?
If you specify the parameters under the [ atomtypes ] section there will 
be default parameters based on combination rules for all possible 
interaction. You can override (some of) these if you have reason to do 
so, like in some cases in the GROMOS force field. You could try to test 
iodine in water to see whether the distances are correct (using g_rdf), 
otherwise I wouldn't worry about it.
> 
> Cheers / Magnus
> 
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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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