[gmx-users] Re: angle constraints

[Thomas Schlesier]

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-request at 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 ?