[gmx-users] Re: angle constraints

[Mark Abraham]

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-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 ?
>