<div>Hi <br></div><div><br></div><div>I am trying to extract bond lengths and bond angles from a trajectory file using g_bond and g_angle. </div><div>Original simulation generated a xtc file which I then converted to pdb using trjconv. </div>
<div><br></div><div>Turns out that for some frames bond lengths (and angles) computed using the xtc file are different from that computed using pdb! And the pdb values are correct as they match with measurements in VMD. Sample outputs for the two cases are below. </div>
<div><br></div><div>Any idea what is causing this discrepancy ? I am using GMX 4.0.5. </div><div><br></div><div>Regards</div><div>Sandeep </div><div><br></div><div><br></div><div><strong>SAMPLE OUTPUT (distance.xvg) </strong></div>
<div><strong><br></strong></div><div>matching values are in bold. </div><div><br></div><div>-------------PDB------------------------</div><div>$ g_bond_d -f propane4.pdb -n bond.ndx -s md.tpr</div><div><br></div><div><font face="courier new,monospace">@ xaxis label "Time (ps)"<br>
@ yaxis label "Distance (nm)"<br></font><font face="courier new,monospace"><strong>0.0000 0.15820</strong><br> 1.0000 0.14859<br> 2.0000 0.17248<br> 3.0000 0.15750<br> 4.0000 0.15835<br> </font><strong><font face="courier new,monospace">5.0000 0.15367<br>
6.0000 0.15394<br> 7.0000 0.15878</font></strong><font face="courier new,monospace"><br> 8.0000 0.15211<br> 9.0000 0.15482<br> 10.0000 0.14874<br></font></div><div><br></div><div><br></div><div><div>-------------XTC------------------------</div>
<div>$ g_bond_d -f propane4.xtc -n bond.ndx -s md.tpr</div><div><br></div></div><div> <font face="courier new,monospace">@ xaxis label "Time (ps)"<br>@ yaxis label "Distance (nm)"</font></div>
<div><font face="courier new,monospace"><strong>0.0000 0.15820</strong><br> 1.0000 0.05791<br> 2.0000 0.13811<br> 3.0000 0.14364<br> 4.0000 0.13509<br> </font><strong><font face="courier new,monospace">5.0000 0.15367<br>
6.0000 0.15394<br> 7.0000 0.15878</font></strong><font face="courier new,monospace"><br> 8.0000 0.06900<br> 9.0000 0.07710<br> 10.0000 0.08916<br></font></div><div><br></div><div><br></div><div><br></div><div><br>
</div><div><br></div>