There is lots of stuff. Please look in manual 7.4 and 8, which bring order to the the morass of available tools.
Mark On Mon, Jul 29, 2013 at 12:29 AM, jayant james <jayant.ja...@gmail.com> wrote: > 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 -- 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
