[gmx-users] g_select dynamic indices

Justin A. Lemkul jalemkul at vt.edu
Wed Nov 30 22:57:25 CET 2011

Yao Yao wrote:
> Hi Gmxers,
> I used g_dist to find all water molecules within 5 Angstrom of a protein 
> in a trajectory with a little surprise that gromacs directly prints out 
> those water on my screen rather than in an output file.

According to g_dist -h, that's what you should expect :)

> Since in each frame, those water molecules are not the same, I realize I 
> need to make a dynamic index or indices for them.
> However I do not see any flag I could possibly introduce those water in 
> g_select and then use -on flag to produce a dynamic index.

The index groups are output by g_select.  Try g_select -select "help all" for 
examples of how to create groups.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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