Hi,
This question has been asked several times before on this list.
The proper way to handle this in Gromacs is to introduce two dummy mass
particles
in such a way the total mass and the moment of inertia is identical to CO2.
Then you can construct the positions of the three mass-less C and O atoms from
the positions of the masses using virtual sites (see the manual).
Berk
> Date: Fri, 10 Jul 2009 16:58:29 +0100
> From: jennifer.willi...@ed.ac.uk
> To: gmx-users@gromacs.org
> CC:
> Subject: [gmx-users] Best way to handle linear rigid molecules.
>
> Hello users,
>
> I am using gromacs v 4.0.5
>
> What is the best way to treat linear triatomic molecules such as CO2.
> Is there some kind of rigid algorthym as in DL_POLY?
>
> In the asbsence of a ?rigid? algorthym. I initially intended to ?fix?
> the C=O bond length using constraints (as below) and somehow ?fix? the
> O=C=O bond angle to 180.
>
>
> [ atomtypes ]
> ; type mass charge ptype c6 c12
> C_CO2 12.01115 0.5406 A 0.0000 0.00000000
> O_CO2 15.9994 -0.2703 A 0.29847 1.10765301
>
> [ moleculetype ]
> ; name nrexcl
> CO2 2
>
> [ atoms ]
> ; nr type resnr residu atom cgnr charge mass
> 1 C_CO2 1 CO2 C_CO2 1 0.5406 12.01115
> 2 O_CO2 1 CO2 O_CO2 1 -0.2703 15.9994
> 3 O_CO2 1 CO2 O_CO2 1 -0.2703 15.9994
>
> [ constraints ]
> ; ai aj funct c0 c1
> 1 2 1 0.12088
> 1 3 1 0.12088
>
> [ angles ]
> ; ai aj ak funct c0 c1
> 2 1 3 1 180.00
>
> First question... How do I go about fixing this angle to 180degrees?
> Should I just make c1 extremely large? Is there a more elegant way of
> going about this? Someone also mentioned using a virtual site
> representation for the C. Any comments on this welcome.
>
> I read some posts which imply that the angle bending code apparently can't
> handle angles of exactly 180 degrees.
>
> http://www.mail-archive.com/gmx-users@gromacs.org/msg09979.html
>
> This was a while ago so perhaps this has been dealt with in the
> current version of gromacs?
>
>
> Thanks
>
>
> --
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> Scotland, with registration number SC005336.
>
>
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