Gmx trjconv for 'selected' trajectories

User discussions
1

GROMACS version: 2021
GROMACS modification: No

Hi,
I am trying to trace the motion of a few fluid molecules that I isolated via gmx selection; my idea is to excract a sub-trajectory containing only the selected atoms:

gmx trjconv -f traj_22ns_26ns.trr -n advl_24.ndx -o advl_24.trr -s system.tpr

and then use it to ‘dump’ a few .gro files:

gmx trjconv -f advl_24.trr -dump 0 -n advl_24.ndx -s system.tpr -o test.gro

However, when I try to do so I get the following error:

Fatal error:
Index[0] 25885 is larger than the number of atoms in the
trajectory file (344). There is a mismatch in the contents
of your -f, -s and/or -n files.

which I believe is due to the fact that system.tpr refes to the whole system, and not to the selection only.
Is there a way to make this work? I would really try to avoid reading through the complete trajectory, as it is particularly heavy. It would be great if there were a direct way to produce a .tpr from the selection to then feed to gmx trjconv, is it somehow possible?

2

Update
I utilized

gmx convert-tpr -s system.tpr -n advl_24.ndx -o system_advl.tpr

to create a corresponding topology; however, if I now run gmx trjconv with the new .trp I get a segmentation fault.

...
Select group for output
Group     0 (resname_SOL_and_x_>_65.7_and_x_<_67.7_and_z_<_30.63400_and_z_>_29.12_f0_t23980.000) has   344 elements
There is one group in the index
Segmentation fault (core dumped)
3

You should be able to directly generate one pdb file with all frames that you can then convert to gro without a tpr. Or you can split the pdb file in separate files for each frame. I don’t know if you can directly generate gro.

1 Like
4

I was hoping to get not only positions, but velocities too.
You thinkall I need to do is to change the output format of the first trjconv to .pdb (or maybe .gro)?

5

Ok, it works with .gro too, now it’s just a matter of separating each fame (but it should be easier).
However, is the segmentation fault expected? Seems like a bug in trjconv

6

A segmentation fault is not completely unexpected, but should never happen.
Can you run this through gdb with a debug build?

7

I can try