[gmx-users] Three-site model for acetonitrile

[David]

On Mon, 2003-02-24 at 20:02, Christoph Freudenberger wrote:
 [ atomtypes ]
> ;type   mass           charge    ptype c6            c12
> MeAN    20.35285       0.000       A   0.90571E-02   0.26212E-04 ; (*)
>   CAN     0.00000       0.000       A   0.51454E-02   0.12167E-04 ; (*)
>   NAN    20.69985       0.000       A   0.26955E-02   0.28943E-05 ; (*)
> 
> [ moleculetype ]
> ; name  nrexcl
> Acetonitril        2
> 
> [ atoms ]
> ;   nr  type    resnr   residu  atom    cgnr    charge  mass
> 1       MeAN     1       MeCN    C1AN    1        0.206  20.35285
> 2       CAN      1       MeCN    C2AN    1        0.247   0.000
> 3       NAN      1       MeCN    N3AN    1       -0.453  20.69985
> 
> [ constraints ]
> ;  ai  aj funct           b0
> 1       3       1          0.26200
> 
> [ dummies2 ]
> ;  ai    aj    ak       funct   a
>      2     1     3       1       0.5572519
> 
> [ exclusions ]
> 1       2       3
> 2       3       1
> 3       2       1
> 
> ;(*) E.Guardia, Mol. Simul. 26, 2001, 2878;
> ;C2AN dummified to keep the molecule linear
> ;-------------eof ---------------------
That looks right. To make sure, you can just use any output conformation
from the simulation and measure the distances in rasmol or something
like that...


-- 
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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