Creating a periodic box programmatically in VMD, with an explicitly specified center

By jdurrant_from_jacobdurrant.com | Published: May 27, 2014

I recently wanted to see if steric clashes at the boundary of a molecular system I’m simulating might be responsible for high-velocity errors. I didn’t want to download the models with the periodic boundary specified because they are enormous, so I discovered how to explicitly specify a periodic box in VMD. My periodic box was centered at {-13.5 -19.5 6.0} and had dimensions of {1308.998 1278.998 1281.998}.

pbc set {1308.998 1278.998 1281.998} -all -molid top
pbc box -center origin -shiftcenter {-13.5 -19.5 6.0}

Not too hard. Hope it helps others looking to do the same thing.

This entry was posted in chemistry. Bookmark the permalink. Post a comment or leave a trackback: Trackback URL.

3 Trackbacks

  • By tadalafil 20mg on November 7, 2020 at 4:11 pm

    cialis tadalafil 20mg

    cialis brand – cialis trackback url for this blog entry – cialis 10mg you cannot post new topics in this forum

  • By viagra for sale cheap on November 7, 2020 at 9:32 pm

    viagra for sale no script

    cialis side effects heartburn guestbook.htm – levitra vs cialis vs viagra reviews guestbook.asp – cheapest cialis

  • By best 918 on November 25, 2020 at 4:11 am

    best 918

    Creating a periodic box programmatically in VMD, with an explicitly specified center – Jacob Durrant

Post a Comment

You must be logged in to post a comment.

  • Categories

  • Archives