[gmx-users] Best way to handle linear rigid molecules.
Jennifer.Williams at ed.ac.uk
Fri Jul 10 17:58:29 CEST 2009
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
[ 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.
This was a while ago so perhaps this has been dealt with in the
current version of gromacs?
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