[gmx-users] exclusions and dummies

[David]

On Mon, 2004-01-26 at 17:32, Dr. Christoph Freudenberger wrote:
> Hi there,
> 
> I was just trying to setup a box of oplsaa chcl3 using
> the following itp:
> [ moleculetype ]
> ; name  nrexcl
> CHCl3     3
> 
> [ atoms ]
> ;   nr   type   resnr  residu  atom    cgnr    charge
>      1   CCL3     1      CHCl3   CT1     1       -0.063
>      2  CLCL3     1      CHCl3   Cl2     1       -0.051
>      3  CLCL3     1      CHCl3   Cl3     1       -0.051
>      4  CLCL3     1      CHCl3   Cl4     1       -0.051
>      5   HCL3     1      CHCl3    H5     1        0.216
> 
> [ constraints ]
> ;  ai    aj funct        b0
>      1     2     1     0.17580
>      1     3     1     0.17580
>      1     4     1     0.17580
>      2     3     1     0.2902831
>      2     4     1     0.2902831
>      3     4     1     0.2902831
> 
> [ dummies4 ]
> ; Dummy from              funct a       b        c
> 5       1   2   3  4      1     0.33333 0.33333 -0.110
> -----------------
> After some errors i looked at the tpr with gmxdump
> a found out that the exclusions for dummies are not
> set automatically.
> I put the exclusions into the itp manually by adding this
> to the above:
> [ exclusions ]
> 5       1   2   3  4
> 
> but i still
> get way to large LJ energies. whats wrong here?
Have you tried minimizing a single molecule? 

By the way, if this is parameterized in official opls, please use the
atom types in ffoplsaanb.itp, so that the topology can also be used to
solvate proteins etc.
> 
> regards
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. 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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