[gmx-users] gmx gangle

João Henriques joao.henriques.32353 at gmail.com
Wed Feb 15 20:34:23 CET 2017

Hello everyone,

It seems that my inquiries about gmx gangle and selections are either too
funky or too basic to justify getting a single answer from the community.
Still, I will try once more with an even simpler scenario, which will
hopefully attract an answer (even if it's just someone telling me to stop
reposting, despite the fact that it is not 100% a repost).

I have a trajectory where the water molecules are ordered by proximity to
the protein. I also have an index file with the N closest waters that I am
interested in analyzing. Now, my plan is to simply compute the O-H angle
distribution within the group composed by these N water molecules. For that
I type something along these lines:

gmx gangle -f xxx.xtc -s xxx.tpr -n xxx.ndx -g1 vector -group1 "group
"hydration_shell" and name OW HW1" -g2 vector -group2 "group
"hydration_shell" and name OW HW1" -oav -oall -oh

To my surprise, this command returns something completely different from
what I expected. Instead of the angular distribution function of all pairs
of O-H vectors from different water molecules, it outputs zero. Obviously,
this means that the command is computing the angle between the O-H vector
of each water molecule and itself. How can I modify my selection to produce
the desired result?

Thank you in advance,
Best regards,

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