From: Norman Geist (
Date: Thu Jan 08 2015 - 03:00:37 CST

What about reading the manual? Section "pbc tools".


And I guess what you want is to see the "wrapped molecule" in VMD. So
assuming you have a protein in water you would do:


pbc wrap -all -compound res -center com -centersel protein


What it does:


wrap = bring atoms back to periodic cell

-all = do it for all frames

-compound res = keep residues together (do not split water etc.)

-center com = move the center of mass of "centersel" to the middle of the
periodic box (as this is the interesting part of the system and shouldn't be

-centersel protein = select "protein" for center of mass alignment


Norman Geist.


Von: [] Im Auftrag von
Sanjib Chowdhury
Gesendet: Donnerstag, 8. Januar 2015 01:53
Betreff: vmd-l: VMD TkConsole command




I want to see the unwrapped molecule in VMD.

I don't know the exact pbc unwrap command.

After loading the molecules in VMD, I have tried with the following
TkConsole command.


pbc unwrap 50.0 21.0 23.0

pbc unwrap a=50.0 b=21.0 c=23.0


These give error.


I will appreciate your help.


Thank you.