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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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