VMD-L Mailing List

From: Manuel Perez Escribano (pesma5_at_alumni.uv.es)
Date: Mon Oct 07 2024 - 12:55:43 CDT

Dear users,

I am facing issues when using pbctools to wrap a trajectory between a periodic nanotube (resname TUBE) and a cyclic macrocycle (resname UNK) which embraces the tube. In my first attempts, I tried "pbc wrap -all -center com -centersel "resname UNK" -compound residue" and I thought it worked fine but I had some frames in which the macrocycle was just too close to the end of the nanotube. I would like to do DFT calculations on top of the structures and I would need the macrocycle and the nanotube to be both centered in the center of the box. I have also tried to wrap with respect to the tube with:

"pbc wrap -center com -centersel "resname TUBE" -compound residue -all"

And then with respect to the macrocycle:

"pbc wrap -center com -centersel "resname UNK" -compound residue -all"

And it did not work in the same way. However, when I do the same but for a specific frame, (with -first and -last flags) it worked. I then tried to do a loop in tcl, wrapping each frame independently, but it seems that it gets info from the previous frame and then the result was again not the one I was seeking for some frames.

What else can I try?

Thank you,

Manuel