[gmx-users] Overriding atomtypes

[David]

On Fri, 2005-01-14 at 18:49 +0000, Nuno R. L. Ferreira wrote:
> Hi *
> 
> Just to be sure.
> Usually, the solvent parameters are placed in a single .itp file.
> If the C6 and C12 parameters are defined in the [atomtypes] field in this
> .itp, the gromp warns that is going to override the atomtype.
> 
> This means, that the LJ parameters are coming from the solvent .itp, right?
> And that all LJ combinations with other atoms (namely protein atoms) are
> going to be performed with these values, spite the f.f. having already those
> combinations in *nb.itp.  That's it?
I suggest you test it by generating two tpr files. First one with all LJ
parameters in the ffXX.itp file, second with additional LJ parameters in
the water file. The you run 
gmxcheck -s first -s2 second | more 

I would strongly advise against having LJ parameters at more than one
place, because you could e.g. by changing the order of the includes get
different parameter sets.
> 
> Regards,
> N.
> 
> 
> ######################################
> Nuno Ricardo Santos Loureiro da Silva Ferreira
> Departamento de Química
> Faculdade de Ciências e Tecnologia
> Universidade de Coimbra
> 3004-535 Coimbra - Portugal
> Fax: +351 239 827703  - www.biolchem.qui.uc.pt
> ########################################
> 
> 
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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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