[gmx-users] nonbonded LJ-parameters

[David van der Spoel]

On Sat, 2005-03-05 at 14:00 +0100, Stephan Dammer wrote:
> Hi,
> 

> ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
> [ nonbond_params]
> ; i     j       func    C_6             C_12
>   GAS   LIQ     1       6.179217664e-5  9.545682736e-8
> ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
> 
> although for GAS-GAS and LIQ-LIQ interactions epsilon and sigma are used.

I think this analysis is correct, and acknowledge that it may be
confusing. Therefore it is important to check what you get after running
grompp, using the gmxdump program. This applies for anything but the
standard pdb2gmx-generated topologies. So:
gmxdump -s topol.tpr | more
and then search for "idef" which is the structure holding the C6 and C12
parameters.


> 
> I posted this, because I do not know if this behavior is wanted (and I
> simply misunderstood the manual), or whether this perhaps should be fixed.
> Moreover, maybe others have stepped upon the same problem.
> 
> Best regards,
> Stephan
> 
> ps: I use GROMACS 3.2.1
> --------------------------------------------------------------------------
> Stephan M. Dammer                             University of Twente
> e-mail: s.m.dammer at tnw.utwente.nl             Physics of Fluids
> web: http://stilton.tnw.utwente.nl/~dammer/   P.O. Box 217, 7500 AE Enschede
> telefone: [+31] (53) 489 2486                 The Netherlands
> fax:      [+31] (53) 489 8068                 room: CT-A 124
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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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

-- 
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++