Hi all,
I was trying to show the bonds between my CG beads in VMD. I have four CG
beads per each molecule, and there are 18 separate molecules which contain
these four beads, which results in having 72 CG beads in total. Therefore,
I expect to see 54 CG bonds in the end.
I used the "coarse_grain.tcl" script to visualize these CG bonds as
suggested on the VMD page. I have two different bead types in the system: CA
and CG. In order to visualize the bonds I used the following command line on
Tk console:
source coarse_grained.tcl
g_cg -tpr topol.tpr -sel {{name "CA"} {name "CB"}} -rep {Licorice Licorice}
-color {name name}
After that it gave me the following lines:
[ g_cg ] Processing "topol.tpr"...
[ g_cg ] Create the bond list for 72 atoms...
[ g_cg ] Rebuild bonds...
[ g_cg ] Create representations...
which I understood that all the bonds are created successfully, but when I
looked at the screen I could see only one of those CG bonds, but not the
others. Why might be the reason?
Thanks in advance
--
Ozge Engin
★☆
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