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

Justin A. Lemkul jalemkul at vt.edu
Wed Apr 21 12:59:14 CEST 2010

swapnil chavan wrote:
> 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 
> <http://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 directory. 
> After copying the gmxdump to /usr/export/gromacs-3.3.3/bin I got another 
> problem i.e.

It's probably better to change the path in the .tcl script, rather than move 
around executables within the root filesystem, but that's just my opinion.

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

What is g_cg?  It's not official Gromacs, but hopefully it comes with some sort 
of documentation as to how to use it.

> 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.

Have you tried top2psf.pl?  Not that coarse_grain.tcl won't work, but it's 
another option.  It's available here:



> Sincerely,
> Neel


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list