[gmx-users] Three-site model for acetonitrile

[David]

On Wed, 2003-02-26 at 17:46, Christoph Freudenberger wrote:
> Anton Feenstra wrote:
>     31.56239       0.000       D   0.0           0.0
> MeAN     0.00000       0.000       A   0.90571E-02   0.26212E-04 ; (*)
>   CAN     0.00000       0.000       A   0.51454E-02   0.12167E-04 ; (*)
>   NAN     0.00000       0.000       A   0.26955E-02   0.28943E-05 ; (*)
> 
> [ moleculetype ]
> ; name  nrexcl
> Acetonitril        2
> 
> [ atoms ]
> ;   nr  type    resnr   residu  atom    cgnr    charge  mass
> 1       D1       1       MeCN    D1AN    1        0.000   9.49031
> 2       D2       1       MeCN    D2AN    1        0.000  31.56239
> 3       MeAN     1       MeCN    C3AN    1        0.206   0.00000
> 4       CAN      1       MeCN    C4AN    1        0.247   0.00000
> 5       NAN      1       MeCN    N5AN    1       -0.453   0.00000
> 
> [ constraints ]
> ;  ai  aj funct           b0
> 1       2       1          0.26300
> 
> [ dummies2 ]
> ;  ai    aj    ak       funct   a
>      3     1     2       1       0.2652197
>      4     1     2       1       0.8203527
>      5     1     2       1       1.2652197
Shouldn't one of these numbers be negative, or is the dummy further out
than the atom?

> 
> [ exclusions ]
> 3       4       5
> 4       5       3
> 5       4       3
> 
> ;(*) E.Guardia, Mol. Simul. 26, 2001, 2878;
> ;A rigid two mass system with the same mom. of inertia
> ;as MeCN is used to provide a linear molecule. Me, C and
> ;N are defined as dummies relativ to D1 and D2.
> ;---------------- eof -------------------
> 
> How does that look...? I will start the new simulation
> as soon as possible
> 
> regards
> -- 
> Christoph Freudenberger
> Abt. Organische Chemie I AK Siehl - Uni Ulm -Tel: ++49-731-502-2785
> 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
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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