On 9/17/17 6:05 PM, Dallas Warren wrote:
http://manual.gromacs.org/documentation/5.1/onlinehelp/selections.html Don't know exactly how to do it myself, but there will be an option there where you can specify the z coordinate as a way to break it up into groups.
And herein lies the challenge. The selections themselves will give index groups per frame, may vary in size, and the individual molecules themselves will likely occupy each slice discontinuously with respect to time. So a lot of effort would have to be made to make per-molecule sub-trajectories to compute a diffusion coefficient for a given time frame in which the molecule continuously satisfies the criterion, then calculated again over another period of time if the molecule moves out and comes back (otherwise one would get a spurious contribution to the MSD if a molecule seems to jump around). I suppose it can be done, but only very tediously in reassembling frames to make sub-trajectories, then looping over every molecule individually in doing so.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html ================================================== -- 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-requ...@gromacs.org.
