Hi I am trying to extract bond lengths and bond angles from a trajectory file using g_bond and g_angle. Original simulation generated a xtc file which I then converted to pdb using trjconv.
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. Any idea what is causing this discrepancy ? I am using GMX 4.0.5. Regards Sandeep *SAMPLE OUTPUT (distance.xvg) * * * matching values are in bold. -------------PDB------------------------ $ g_bond_d -f propane4.pdb -n bond.ndx -s md.tpr @ xaxis label "Time (ps)" @ yaxis label "Distance (nm)" *0.0000 0.15820* 1.0000 0.14859 2.0000 0.17248 3.0000 0.15750 4.0000 0.15835 *5.0000 0.15367 6.0000 0.15394 7.0000 0.15878* 8.0000 0.15211 9.0000 0.15482 10.0000 0.14874 -------------XTC------------------------ $ g_bond_d -f propane4.xtc -n bond.ndx -s md.tpr @ xaxis label "Time (ps)" @ yaxis label "Distance (nm)" *0.0000 0.15820* 1.0000 0.05791 2.0000 0.13811 3.0000 0.14364 4.0000 0.13509 *5.0000 0.15367 6.0000 0.15394 7.0000 0.15878* 8.0000 0.06900 9.0000 0.07710 10.0000 0.08916
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
