[gmx-users] water molecules (interfacial)

Mark Abraham Mark.Abraham at anu.edu.au
Sat Nov 13 16:47:08 CET 2010

On 14/11/2010 12:21 AM, atila petrosian wrote:
> Dear Mark and gromacs users
> thanks for your time and attention.
> how to make selection.dat file? what should be in that?
> please clarify this new tool more. how can I obtain what I need 
> (number of water molecules (interfacial) to be within
> 2.4 A distance from both the protein and the ligand during simulation. 
> also, exact numeration of each water being
> in interface between protein and ligand)?

IIRC g_select has some better documentation available once you run it 
and ask for help, somewhat like make_ndx.


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