On 2/15/19 4:10 AM, Apramita Chand wrote:
Dear Gromacs Users, I have two kinds of molecules in my system. I want to know the coordinates of the molecule A that is found closest to molecule B at every snapshot of the MD trajectory. I am using gromacs 5.1. I dont have a cutoff, I just want to generate coordinates of the single one molecule that is closest at any given snapshot.(for all frames0 How do I do so? Is there any gmx tool? I tried '-select' statements but am not able to hit upon the right combination.
You can use gmx trjorder to reorder the molecules in the trajectory based on their proximity to some selected group. Then just write out the first instance of that molecule from the trajectory using an index group (the closest molecule will always be the first one of its type so the index group is constant, even if it is selecting a different molecule).
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== -- 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.
