Dear Shayantani, The output you quote show a negative potential energy. Is that not for the run you refer to?
(With regards to “Hello Sir”, may I suggest a more gender inclusive greeting.) Kind regards, Erik ______________________________________________ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 23 Feb 2018, at 19:32, SHYANTANI MAITI <shyantani.ma...@gmail.com<mailto:shyantani.ma...@gmail.com>> wrote: Hello Sir, When I go for energy minimization for a protein complex containing 3 proteins, I obtain potential energy being minimized upto zero from positive. The potential energy is not becoming negative even after running for many steps as viewed in potential.xvg obtained after energy minimzation. Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------ ------------------- Potential -6.06412e+06 1.2e+06 5.52222e+07 -7.26522e+06 (kJ/mol) Is the energy minimization considerable for further equilibration or do I need to obtain only negative energy and after that only should I start my equilibration? Does the value of potential energy obtained after minimization need to be negative in all cases? Can I continue my equilibration with this result? Thanking you -- Best regards, *Shyantani Maiti* -- 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<mailto: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.