Gmx trjconv giving trajectory file with zero values in y and z coordinates

GROMACS version: 2021.1
GROMACS modification: Yes/No
Dear colleagues,
I have done clustering with 1,2- hexanediol molecule using gmx cluster and got a index file out put from cluster frames. Using that index file when I am extracting the cluster members as a trajectory using trajcov I am getting the output file but it doesn’t have any y and z coordinates. It’s showing 0 for all. So the molecules when I am opening in pymol is showing one rod like structure. For many file I have used same procedure but I never got such error. Input file I have checked but its not showing any error it have all the coordinates. I am not able to find the mistake. Please help me with this.

Actually I have resolved the problem. Problem was with the input file. There was a problem of proper spacing so it couldn’t extract the files properly.

But I am surprised how gmx clustering was run successfully with this input. How it has given the clusters?

Hi, can you list the commands you used and indicate in which file the issue occured? The .ndx output from gmx cluster is in the .ndx format but it contains frame numbers instead of atom indices, so that’s a bit unusual. Is your point that the frame numbers were so high that they got concatenated, or was there a problem with the (independently produced) .ndx you input into gmx cluster?

In gmx cluster there is a flag -clndx it writes the frame numbers corresponding to the clusters to the specified index file to be read into trjconv. I have used that .ndx file and used to extract those frames in gmx trjconv module with -fr flag.