[gmx-users] Slicing .gro file geometry

Mark Abraham Mark.Abraham at anu.edu.au
Thu Aug 18 16:46:32 CEST 2011

On 19/08/2011 12:43 AM, shikha nangia wrote:
> Dear all:
> I would like to create a smaller simulation box (from a larger 
> simulation box in .gro file) by removing atoms in the x, y and 
> z-directions and saving the subset system into a new .gro file 
> (smaller box and subset of molecules)
> For example: from original box 10x10x10 nm3 write coordinates of the 
> atoms that form 5x5x 5 nm3 core of the larger cube.
> I tried editconf and trjconv but they both do not have any such 
> option. Is there another utility in gromcas that can do this?

No. You would need to write a script to do this.

The vast majority of existing tools work "from the ground up" because 
that is the normal scenario. I suggest you explore how to work in that way.

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