[gmx-users] Re: hkl harker sections

[Mark Abraham]

On 1/04/2012 12:12 AM, lloyd riggs wrote:
> Hello all,
>
> Does anyone know where to look to do a slice of my unit cell along sections (energies, forces etc...)  or to just give a list of all atoms in the slice.  Something like an h,k,l or x,y,z slice through a section.

You can use g_select to create an index group based on geometric 
criteria to use as input to any of the other tools, but any such index 
group is only applicable to the frame that generated it, because 
diffusion will occur. Proper dynamic selections are planned for future 
GROMACS releases. Meantime, you'd have to script g_select to feed index 
groups to your analysis tool of choice.

Mark