[gmx-users] defining a group within a cutoff

Yunfeng Hu yunfeng at scripps.edu
Tue Oct 12 23:29:47 CEST 2004

Hi, I wonder if anyone can give a clear answer of how to use trjorder 
and/or other commands to define an index.ndx file which can be used for 
h_bond analysis purposes. Thanks.


P.S. trjorder -h is not very helpful.

On Tue, 2004-10-12 at 00:55, Yunfeng Hu wrote:
> Hi, I am trying to analyze the number of hydrogen bonds between small
> ligand and surrounding water/enzyme from a md simulation. However there
> are ~10,000 water molecules and  g_hbond ran out of memory. As a matter
> of fact, I am only interested in the water near the ligand. Is there a
> way that I can define a group (including protein and water) centered
> within 5 angstrom of the ligand? I have yet figured out how to use
> make_ndx to do this. Thanks.

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