[gmx-users] merge many boxes

Justin Lemkul jalemkul at vt.edu
Thu Jan 17 02:53:26 CET 2013

On 1/16/13 8:26 PM, Kieu Thu Nguyen wrote:
> @Justin, i am trying to simulate oligomerization of membrane protein. I
> want to assemble a big box with proteins from many small box having a
> protein. Is it available ?

The method I described previously should work.  You place one patch (membrane + 
embedded protein) at some location within a large box using editconf -center, 
then combine with any other system(s) that have similarly been positioned using 
editconf -center.  The tutorial I linked before demonstrates a trivial example 
of something similar, but it illustrates the logic behind the process.  You 
won't get any clashes to be automatically resolved/molecules deleted, but even 
with small gaps or unequilibrated boundaries, a gentle equilibration protocol 
should resolve those issues.



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


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