[gmx-users] Three-site model for acetonitrile

[Christoph Freudenberger]

Hi David,

David wrote:
> This is why I was aking about how you keep it linear. The angle will not
> work, or will be rather instable at best, since the potential is not
> continuous at 180 (i.e. angle <= 180 always). You probably want to
> define the C as a dummy particle. Note that you will have to
> redistribute the mass over N and CH3 such that centre of mass is
> unchanged and inertia tensor is not modified too much either.

I just read anything about constraints and dummies in the manual and i
think i'm beginning to understand the concept.
Does this topolgy make sense?

;------------------------------
[ 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 ---------------------

regards
-- 
Christoph Freudenberger
Abt. Organische Chemie I AK Siehl - Uni Ulm -Tel: ++49-731-502-2785