VMD-L Mailing List
From: Sanjib Chowdhury (sanjib_at_udel.edu)
Date: Thu Jan 08 2015 - 10:27:51 CST
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Dear Norman,
It is working with the following commands
pbc set {506.864 20.76 23.4 90 90 90} -all
pbc unwrap
Many thanks for your time and help.
Best,
Sanjib
From: Norman Geist [mailto:norman.geist_at_uni-greifswald.de]
Sent: Thursday, January 08, 2015 10:17 AM
To: 'Sanjib Chowdhury'
Cc: VMD Mailing List
Subject: AW: vmd-l: VMD TkConsole command
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 [mailto:sanjib_at_udel.edu]
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.
Sanjib
From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] 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
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
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