On 4/11/18 7:13 AM, Harry Mark Greenblatt wrote:
BS”D In a given system with several chains, after minimisation the chains are split up by PBC. Using trjconv on this file to put all the chains back into a unified complex, the Ions are converted to water molecules. The input file (-f) and the reference file (-s) had waters and Ions (sodium and chloride), but the output file has only waters (waters have replaced the ions). Seems to be a bug.
That seems wildly unlikely, but there's no way to know unless you can provide actual details: GROMACS version? input files? exact command used?
-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.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.