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 directory. 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. Sincerely, Neel
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