[gmx-users] "coarse_grain.tcl" script does not show all of the coarse-grained bonds in vmd

Nicolas Sapay nicolas.sapay at cermav.cnrs.fr
Thu Dec 3 10:54:28 CET 2009

Ozge Engin a écrit :
> 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}

you mentionned that you have 2 types of beads called CA and CG. Here, 
you are selecting beads named CA and CB. Maybe that's where the problem 
come from. Try to modify the representations manually (from the 
"representation" menu) to see if it change something. If not, that is 
probably a bug in the parsing of the gmxdump output. That is where the 
bonds come from.

> 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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