[gmx-users] how to model linear rigid molecules (CO2)

Kiwoong Kim ilmarekw at gmail.com
Tue Jan 10 14:47:51 CET 2012


I need to model linear rigid molecules, CO2.
I understood that the virtual site have to be introduced to model CO2
like below way.

[ atomtypes ]
;   type      mass    charge    ptype       c6            c12
    D1         22.004975        0.0000       A         0.0000      0.00000000
    D2          22.004975       0.0000       A         0.0000      0.00000000
    C_CO     0.0000000          0.5406       V         0.0000      0.00000000
    O_CO     0.0000000         -0.2703       V         0.29847   1.10765301

[ moleculetype]

However, my question is that I don't know how to give coordinates of
dummy particle to the initial coordinate file(i.e., my pdb file) which
already has coordinates of C, O, and O but not dummy particle yet.
My simulation case is not standard, so pdb2gmx is not working. I have
to build each file by hand.
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