VMD-L Mailing List

From: Daniel Möller (daniel.moeller3_at_uni-greifswald.de)
Date: Fri Apr 01 2016 - 03:10:31 CDT

Hi,

 

did you try:

 

pbc box -center com -centersel protein

?

 

Sincerely

 

Daniel Möller

 

 

 

Von: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] Im Auftrag von Ky Wildermuth
Gesendet: Freitag, 1. April 2016 02:15
An: vmd-l_at_ks.uiuc.edu
Betreff: vmd-l: issue drawing a PBC box centered on a selection

 

Hello, the system that I am working with includes a protein interacting with a lipid membrane in water. Using the pbctools plugin, I am trying to draw a box of the unit cell size but centered on the center of mass of the protein instead of the origin of the system. After loading the dcd and psf file, the size of the box seems correct by default but my problem is getting the box to be centered on an atom selection.

 

These commands seem to work properly:

$pbc box -center com

$pbc box -center bb

$pbc box -center origin

 

However the following commands only create a box centered at the same default location that is not the center of the system nor the center of my selection and the box properties do not change from frame to frame.

 

$pbc box -center unitcell

or

$set sel [atomselect top "protein"] #or any other selection

$pbc box -centersel sel

 

You can see the default box location that I am talking about in the following image (protein in red, lipid in green, water not shown):

http://3.1m.yt/9dLwD3D.jpg

Again, this is the same box location for both the unitcell option and any atom selection, which seems odd to me. I suspect that it is not a problem with defining the unit cell because the box size is by default appropriate, and the dcd files should provide the necessary pbc information, right?

 

I have tried various selection methods and other troubleshooting. Hopefully I am just making a simple error and someone can guide me in the right direction. Please advise and thank you very much!

 

-Kyle