[gmx-users] merge many boxes
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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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