Dear gmx,
I am simulation a kinase protein which has (~1200 aa) length. When I energy minimize the protein with default em file from Justin A. Lemku tutorial. i have got the following output. writing lowest energy coordinates. Steepest Descents converged to Fmax < 1000 in 1162 steps Potential Energy = -4.6686910e+06 Maximum force = 9.6213324e+02 on atom 10673 Norm of force = 1.6875889e+01 After i plot the potential and through " gmx energy -f em.edr -o potential.xvg " by selecting potential (15) and 0, i end up with following results.. Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- Potential 1.97914e+09 2e+09 5.83904e+10 -1.18272e+10 (kJ/mol) When i try to see this value in xmgrace plot, i ccouldnt see any plot. Doesnt mean my system is not relaxed well? Should i need to increase the steps of em ? if so, how do i ? Thanks. -- 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.
