From: Norman Geist (norman.geist_at_uni-greifswald.de)
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
splitted)

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

 

Norman Geist.

 

Von: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] Im Auftrag von
Sanjib Chowdhury
Gesendet: Donnerstag, 8. Januar 2015 01:53
An: vmd-l_at_ks.uiuc.edu
Cc: johns_at_ks.uiuc.edu
Betreff: vmd-l: VMD TkConsole command

 

Hi

 

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.

Sanjib