[gmx-users] can't see bonds between my CG beads in VMD

swapnil chavan neel.niper at gmail.com
Wed Apr 21 12:53:42 CEST 2010

Hi all,
I am running coarse grain MD simulations first time and unable to see bonds
after loading .gro and .trr file in vmd.
I have made initial .pdb by atom2cg.awk, then .itp by seq2itp.pl. With use
of this, I prepared .pdb ,.itp and .top and subjected to mdrun. During
analysis in vmd I can't see any bond among this grains. I have used
coarse_grained.tcl to make it possible but I got error of
- couldn't execute "/usr/export/gromacs-3.3.3/bin/gmxdump": no such file or
After copying the gmxdump to /usr/export/gromacs-3.3.3/bin I got another
problem i.e.
g_cg -tpr min.tpr

[ g_cg ] Processing "min.tpr"...
can't read "N": no such variable

Can anyone please let me know whether I am correctly doing this coarse grain
md. Please guide me to analyse my trajectory of coarse grain md in which I
can't see anything except beads. Your help will be deeply regarded.
Thank you in advance.

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