On 25/07/2012 10:08 PM, Thomas Schlesier wrote:
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)
One should want to get both the total mass and the moment of inertia
correct...
http://lists.gromacs.org/pipermail/gmx-users/2003-September/007095.html.
Mark
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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