<++>-----------------------------------------------------------------------<++> <++> mdgx: A molecular dynamics engine in the AMBER suite of programs <++> <++> <++> <++> Written by David S. Cerutti, Case Group (2009) <++> <++>-----------------------------------------------------------------------<++> Run on Fri Feb 14 23:14:18 2020 <++>-----------------------------------------------------------------------<++> INPUT LINE TEXT: mdgx -O -i cfsamp_II.in INPUT FILE TEXT: &files -p HID.top -c HID.crd -o cfsamp_II.out &end &configs % Backbone phi and psi sampling GridSample :2@C :3@N :3@CA :3@C { -180.0 180.0 } fbhw 10.0 Krst 64.0, GridSample :3@N :3@CA :3@C :4@N { -180.0 180.0 } fbhw 10.0 Krst 64.0, % Make sure that the backbone does not form hydrogen bonds with itself Set :1@O :2@H { 50.0 50.0 } fbhw 47.5 Krst 64.0, Set :1@O :3@H { 50.0 50.0 } fbhw 47.5 Krst 64.0, Set :1@O :4@H { 50.0 50.0 } fbhw 47.5 Krst 64.0, Set :1@O :5@H { 50.0 50.0 } fbhw 47.5 Krst 64.0, Set :2@O :3@H { 50.0 50.0 } fbhw 47.5 Krst 64.0, Set :2@O :4@H { 50.0 50.0 } fbhw 47.5 Krst 64.0, Set :2@O :5@H { 50.0 50.0 } fbhw 47.5 Krst 64.0, Set :3@O :4@H { 50.0 50.0 } fbhw 47.5 Krst 64.0, Set :3@O :5@H { 50.0 50.0 } fbhw 47.5 Krst 64.0, Set :4@O :5@H { 50.0 50.0 } fbhw 47.5 Krst 64.0, RandomSample :3@CG :3@CB :3@CA :3@N { -180.0 180.0 } Krst 16.0, RandomSample :3@ND1 :3@CG :3@CB :3@CA { -180.0 180.0 } Krst 16.0, combine 1 2, count = 64, verbose 1, maxcyc = 5000, strainlim = 20.0, bstrain = 10.0, astrain = 10.0, % Reshuffling nshuffle = 2, shuffle bootstrap, % Output controls outbase 'Conf', 'Conf', write 'cdf', 'pdb', outsuff 'cdf', 'pdb', &end <++>-----------------------------------------------------------------------<++> <++>-----------------------------------------------------------------------<++> (1.) Energies of the initial and final states. Units are kcal/mol. A number of statistics could be of interest here: this table tries to anticipate them. Statistic Mean Value Std. Dev. Min. Value Max. Value (kcal/mol) (kcal/mol) (kcal/mol) (kcal/mol) ------------------------ ------------ ------------ ------------ ------------ Initial E(Model) (a) 42.3151 0.0000 42.3151 42.3151 Initial E(Restraint) (b) 267.8498 81.6576 65.7286 446.3166 Final E(Model) (c) -6.1058 8.6703 -17.2554 46.9731 Final E(Restraint) (d) 5.1452 14.6429 0.1994 108.6979 Delta E(Model) (e) -48.4209 8.6703 -59.5705 4.6580 Delta E(Restraint) (f) -262.7046 82.6965 -445.5973 -63.4664 Reoptimization (g) -60.9010 109.1931 -427.1280 0.0000 (a) The energies of the initial models, without the restraint energy (this is an indicator of how strained the configurations were before mdgx began to manipulate them). (b) When restraints were first applied to the initial models, these were the restraint energies. (c) The energies of the final models, again excluding restraint energy. This is an indicator of how strained the molecular configurations became after manipulation. (d) Restraint energy needed to get the final configurations into place. (e) This is an indicator of the change in molecular mechanics energy. E(model) will typically rise, indicating that structures became distorted in response to pressure from external restraints. (f) The change in restraint energy. E(restraint) will typically fall as restraints force the structures into new configurations. (g) Reoptimization was performed by bootstrap, randomly swapping solutions to different restraint sets and using them as the initial states in subsequent energy minimizations. If this drove the energy down relative to the previous solution, the result was retained. <++>-----------------------------------------------------------------------<++> <++>-----------------------------------------------------------------------<++> (2.) Convergence statistics for the run. This block of information describes the energy minimization of ALL configurations, regardless of whether they were printed. The next section presents counts of configurations passing the basic sanity checks. These convergence statistics pertain to the final round of optimization performed after 2 rounds of reshuffling. - Average steps to convergence: 1522 +/- 536 - Total converged configurations: 64 - Unconverged configurations: 0 - Successful reoptimizations: 33 - Configs with reoptimizations: 29 <++>-----------------------------------------------------------------------<++> <++>-----------------------------------------------------------------------<++> (3.) Basic sanity checks. If a configuration fails these tests, it was not printed out for further consideration but the reasons it failed will be summarized here. The tests are that, first, no bond of a configuration may be strained more than 10.00 kcal/mol. Furthermore, no angle may be strained more than 10.00 kcal/mol. Finally, the maximum tolerated restraint energy (summed over all restraints) is 20.00 kcal/mol. If any of these tests seem too stringent or not tight enough, the thresholds may be changed in the &configs namelist. - Configurations passing all sanity checks: 60 - Configurations failing bond sanity check: 0 - Configurations failing angle sanity check: 0 - Configurations failing restraint sanity check: 4 Descriptions of each problematic configuration follow, along with the names and numbers of atoms involved in each feature creating the problem. - Configuration 19: Total restraint energy 108.6979 Restraint binding atoms ND1 -CG -CB -CA (25, 24, 21, 19) strained to 86.9997 - Configuration 38: Total restraint energy 20.3365 Restraint binding atoms CG -CB -CA -N (24, 21, 19, 17) strained to 19.9072 - Configuration 51: Total restraint energy 30.4984 Restraint binding atoms CG -CB -CA -N (24, 21, 19, 17) strained to 29.4815 - Configuration 55: Total restraint energy 37.5978 Restraint binding atoms CG -CB -CA -N (24, 21, 19, 17) strained to 36.2307 <++>-----------------------------------------------------------------------<++>