From: Sanjib Chowdhury (sanjib_at_udel.edu)
Date: Thu Jan 08 2015 - 15:22:31 CST

Hi,

 

Coordinates are wrapped since I used PBC. In PBC, when atoms cross the
boundary their mirror images enter into the system from opposite sides.

As results, I can’t see the actual deformation/trajectory without unwrapping
it.

 

Thanks,

Sanjib

 

From: Daniel Möller [mailto:daniel.moeller3_at_uni-greifswald.de]
Sent: Thursday, January 08, 2015 3:14 PM
To: 'Sanjib Chowdhury'
Cc: vmd-l_at_ks.uiuc.edu
Subject: AW: vmd-l: VMD TkConsole command

 

Hi,

 

I just want to ask, why your coordinates are wrapped, so that you have to
unwrap them?

 

Greetings

 

Daniel

 

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 17:28
An: 'Norman Geist'
Cc: vmd-l_at_ks.uiuc.edu
Betreff: RE: vmd-l: VMD TkConsole command

 

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