On 10/2/17 11:14 PM, Dallas Warren wrote:
Thanks for the reply Justin. I am just going to use the largest exclusion bond distance I can, then ignore the RDF of those beyond that distance. Seems curious to me (not actually understanding what grommp is generating) that the list is so large. These are linear molecules, 38 atoms, 60 molecules in total.
It generates a matrix of all possible exclusions, sorts them, then removes duplicates. So for nrexcl = 37 you need memory on the order of 37 * 37 * 60 * (2 * sizeof(int)) - the factor of 2 for the atom numbers comes from the fact that you're actually allocating an array of type "sortable" which is a pair of atom numbers.
-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.
