Thanks to mark for his explanations. We performed MD simulation on a peptide fragment as well as its mutants where, its residues have been systematically replaced by alanine residue. We found that potential and kinetic energies of one mutant (T=>A) is significantly different from other molecules. interestingly there are other similar substitutions in different positions indicating that molecules with similar masses and chemical formula are being compared. apparently, we are facing with an special case in which the changing of the position of a residue has profound effect on the kinetic and potential energies. our question is related to the interpretation of this finding!! Regards Emran
On Sun, Jun 25, 2017 at 2:45 AM, Emran Heshmati <compbi...@gmail.com> wrote: > Dear Gromacs users > I performed alanine scaning mutagenesis using gromacs on a peptide > fragment consisting 16 aa. In one of the mutations, the kinetic energy of > the system was significantly different. How can I interpret this result? > any comment is welcome > regards > Emran > -- 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.