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].
