Hi João,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!
Best, Antonio 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, João -- 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 [email protected].
-- 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 [email protected].
