[gmx-users] merge many boxes

[Justin Lemkul]

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:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/biphasic/index.html

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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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