[gmx-users] merge many boxes

Justin Lemkul jalemkul at vt.edu
Wed Jan 16 17:12:06 CET 2013

On 1/16/13 10:09 AM, Kieu Thu Nguyen wrote:
> Dear All,
> I want to merge two or many boxes with the same size into one new box. The
> size of new box is not a multiples of old box size. And the molecules that
> overlap have to be removed. In Gromacs, are there any tool for my problem ?

See the logic of constructing heterogeneous systems here:


You can position one component anywhere in a unit cell with editconf -center, 
and potentially fill the other half with a solvent using genbox -cs, which will 
remove overlapping molecules, but any system more complex than stacking a few 
boxes in the same dimension will not be very easy.  With the editconf -center 
method, one could conceivably place any number of boxes anywhere in the unit 
cell, but there is no automatic removal of overlapping atoms.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list