[gmx-users] pdb vs xtc with g_bond and g_angle

[sandeep somani]

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
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