Hi all, 1) I am looking at see if two adjacent helices are changing their conformation in space. I would like to monitor whether they are orthogonal to each other or have become parallel to each other during simulations. Is it possible in Gromacs to follow such changes, and if so, what command would I use to track such changes?
2a) Also how would I track domain rotations? To check if a domain A is rotating with respect to domain B. I am thinking of picking 2 amino acids on domains A and B and monitor the dihederal angle to see if there is rotation between domains A and B. Is it possible to do such an analysis using Gromacs and if so how and what command should I be using? or if there is a different way please do share. 2b) Also I am looking to monitor whether domain A is in the same plane as domain B or if it has gone up or down in space with respect to domain B? How can I monitor this feature? I appreciate your help. Thank you James -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
