VMD-L Mailing List
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
-centersel protein = select "protein" for center of mass alignment
Von: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] Im Auftrag von
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
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.