Dear Yvon, Are you sure you ‘re not constraining, say, H-bonds in one and not the other?
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 28 Mar 2017, at 07:55, Yvon Wong <wong.y...@gmail.com<mailto:wong.y...@gmail.com>> wrote: I try to compare the energy in CHARMM and GROMACS. After running 4 systems I found the dihedral energies are the same, but the bond energies are different. Can somebody help me to solve this problem? (1)Only one residue: MET Bond: 0.44*4.18 = 1.839 (CHARMM) ====> 2.587 (GROMACS) (different) Dihedral: 3.687* 4.18 = 15.4116 (CHRAMM) ====> 15.4448 (GROMACS) (the same) (2)Only one residue: GLY BONDS: 0.34243*4.18= 1.431 ===> 1.209 Dihedrals 1.77911*4.18 = 7.436 ===> 7.447 (3)5 -residue: ASN GLY PHE TRP THR BONS: 4.82777* 4.18= 20.1800 ====> 22.58 DIHE: 37.82747*4.18 = 158.1188 ====> 158.504 (4)20- residue: GLY LYS MET PHE SER TRP TYR VAL ALA ARG CYS VAL PRO TRP MET SER SER LYS LYS MET BONDS 17.48049 * 4.18 = 73.068 =======> 78.64 DIHE 185.71 * 4.18 = 776.26 =======> 777.32 -- 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.