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

[Jennifer Williams]

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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