What you have done there looks very strange...
easiest wy would be:
define the two oxygens as normal atoms (1,2), give them a bondlength twotimes the C-O bond length define the carbon as a dummy (3), while you construct it's position from both oxygens with a=0.5
one thing i don't know is how to handle the mass:
1) give both oxygen half of the system mass
2) give all atoms their normal mass
would tend to (2)

greetings
thomas

Am 25.07.2012 13:15, schrieb gmx-users-requ...@gromacs.org:
How to choose the positions of the dummy atoms while constraining the
angle for a linear triatomic molecule?
The topology for a such molecule ( af for example CO2 ) is as follows

[ moleculetype ]
; Name            nrexcl
CO2      2

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass
typeB    chargeB      massB
; residue 503 CO  rtp CO   q  0.0
      1         D1    503     CO     D1      1          0      21.90158
   ; qtot 0
      2         D2    503     CO     D2      2          0      21.90158
   ; qtot 0
      3         CE    503     CO     CO      3        0.7       0.00000
   ; qtot 0.7
      4         OE    503     CO    OC1      4      -0.35       0.00000
   ; qtot 0.35
      5         OE    503     CO    OC2      5      -0.35       0.00000
   ; qtot 0.35
[ constraints ]
;  ai  aj funct           b0
1 2 1   0.2000

[ dummies2 ]
;  ai    aj    ak       funct   a
     3     1     2       1       0.0170
     4     1     2       1       0.1000
     5     1     2       1       0.2170


[ exclusions ]
3 4 5
4 5 3
5 4 3



The .rtp file for CO2

[ CO ]
  [ atoms ]
     D1     D1          0.0000           1
     D2     D2          0.0000           2
     CO    CE          0.7000           3       
     OC1  OE         -0.3500    4       
     OC2  OE         -0.3500            5       
  [ bonds ]
     CO   OC1
     CO   OC2


Can anyone please check above file parts whether I'm doing correct or not ?

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