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}
Hi,
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.
Cheers,
Nicolas
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
★☆
<>--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
