Hi all,<br><br>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. <br>
<br>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:<br>
<br>source coarse_grained.tcl<br>g_cg -tpr topol.tpr -sel {{name "CA"} {name "CB"}} -rep {Licorice Licorice} -color {name name}<br><br>After that it gave me the following lines:<br><br>[ g_cg ] Processing "topol.tpr"...<br>
[ g_cg ] Create the bond list for 72 atoms...<br>[ g_cg ] Rebuild bonds...<br>[ g_cg ] Create representations...<br><br>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?<br>
<br>Thanks in advance<br>-- <br>Ozge Engin<br> ★☆<br>