<div class="gmail_quote">Hi all,<div>I am running coarse grain MD simulations first time and unable to see bonds after loading .gro and .trr file in vmd. </div><div>I have made initial .pdb by atom2cg.awk, then .itp by <a href="http://seq2itp.pl" target="_blank">seq2itp.pl</a>. 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 </div>
<div>- couldn't execute "/usr/export/gromacs-3.3.3/bin/gmxdump": no such file or directory. </div><div>After copying the gmxdump to /usr/export/gromacs-3.3.3/bin I got another problem i.e.</div><div>g_cg -tpr min.tpr</div>
<div><br></div><div>[ g_cg ] Processing "min.tpr"...</div><div>can't read "N": no such variable</div><div><br></div><div>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.</div>
<div>Thank you in advance.</div><div><br></div><div>Sincerely,</div><div>Neel</div>
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