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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