VMD-L Mailing List

From: Leonardo Trabuco (ltrabuco_at_ks.uiuc.edu)
Date: Mon Apr 16 2007 - 16:56:15 CDT

On Mon, Apr 16, 2007 at 04:46:48PM -0400, Margaret S. Cheung wrote:
> Hello,
>
> We are trying to solvate an asymmetric molecule and we would like to use
> a "cubic" periodic boundary box in which the box length is determined by
> the largest edge to edge distance of this molecule. We tried to avoid
> the "padding" approach, else it will give us a rectangular box if
> following the VMD solvate tutorial.

You can specify the box size in the VMD solvate GUI.

Best,
Leo 

-- 
Leonardo Trabuco, Ph.D. student
Theoretical and Computational Biophysics Group
University of Illinois at Urbana-Champaign