VMD-L Mailing List

From: Ky Wildermuth (kywildermuth_at_gmail.com)
Date: Thu Mar 31 2016 - 19:14:48 CDT

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