Dear Abid, I wouldn’t call it an issue nor an error. Your protein is still interacting with some periodic copy of the solvent molecules. See http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions.
Kind regards, Erik On 27 Apr 2016, at 05:23, Abid Channa <abid_chann...@yahoo.com<mailto:abid_chann...@yahoo.com>> wrote: Dear Gromacs users, I have run 40 ns simulation , after 20 ns simulation my protein is continuously jumping from water Box. Is there any periodic boundary conditions issue with my system or an other error is that . Kindly give your valuable remarks. Thanks, Regards, Abid Ali Channa, Junior Research Fellow, Lab No. P-133, Computational Chemistry Unit, Dr .Panjwani Center for Molecular Medicine and Drug Research (PCMD), International Center for Chemical and Biological Sciences (ICCBS), University of Karachi-75270.Karachi-Pakistan.UAN # (92-21) 111-222-292 Ext. (309) Cell # +923013553051. http://www.iccs.edu/ -- 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. -- 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.
