[gmx-users] Best way to handle linear rigid molecules.

[Berk Hess]

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.Williams at ed.ac.uk
> To: gmx-users at 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
> 
> 
> -- 
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
> 
> 
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