From: Norman Geist (
Date: Thu Jan 08 2015 - 09:17:15 CST

Yeah, your post lacks of detail. A XYZ doesn't contain box information, you
need to set it manually before wrapping:


pbc set {506.864 20.76 23.4 90 90 90} -all


Are you sure this is your box size? In your 1st post you mentioned


a=50.0 b=21.0 c=23.0


Norman Geist.


Von: Sanjib Chowdhury []
Gesendet: Donnerstag, 8. Januar 2015 15:51
An: 'Norman Geist'
Cc: 'VMD Mailing List'
Betreff: RE: vmd-l: VMD TkConsole command


Dear Norman,


Thanks for your comments/suggestions.

I have checked the VMD manual and also tried with the options you mentioned.

I am getting error in the Tkconsole.


I have attached my file for your kind checking.

The model has the following dimensions -


a=506.864, b=20.76, c=23.4, alpha=90, beta=90, gamma=90.


I will appreciate your further comments/suggestions.


Thank you.



From: [] On Behalf Of
Norman Geist
Sent: Thursday, January 08, 2015 4:01 AM
To: 'Sanjib Chowdhury'
Cc: VMD Mailing List
Subject: AW: vmd-l: VMD TkConsole command


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.