[gmx-users] gmx gangle
baptista at itqb.unl.pt
Wed Feb 15 23:37:20 CET 2017
I used gangle to compute several angle distributions relative to the
z-axis membrane normal, but that was almost a year ago, so I don't recall
the details. But I can tell you that, after many failed attempts, I gave
up from using fancy stuff in the -group1 and -group2 options. Instead, I
ended up writing a small bash script to process one atom pair at a time
(just one group in the .ndx file per gangle run) and to collect everything
at the end.
I understand that your problem is a bit different (your second vector is
not an axis, but defined by a second atom pair), but maybe a similar
"minimalist" approach could get the job done. Or not... Good luck!
On Wed, 15 Feb 2017, João Henriques wrote:
> 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,
> Gromacs Users mailing list
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users