Hi,
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]
.
.
.
etc.
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.
Thx.
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