File generated by QwikMD (version 1.1) on 18:43-CDT, 09/30/2016 Machine name: bangui.ks.uiuc.edu (Linux). ============================================================================== QwikMD text log file. In this file one can find the steps taken to prepare, perform and analyze the MD simulation. The file is divided in 3 major sections: "Structure Preparation" lists the operations performed to prepare the structure for simulation, such as atom deletion and residue renaming; "MD Protocols" lists the MD simulation protocols prepared/performed and their specific parameters like temperature, and simulation time; "MD Analysis" list the analysis performed to the trajectory generated by the execution of the previous MD protocols. ============================================================================== ============================== Structure Preparation =============================== The structure 1QHJ was loaded directly from PDB website. The original structure can be found at /Scr/scr-test-trudack/A-modul/1qhj/new_vacuum_0930/1qhj_vacuum/setup/1QHJ_original.pdb The following residues were deleted: The Residue name PH1, id 500 from chain A The Residue name PH1, id 501 from chain A The Residue name PH1, id 502 from chain A The Residue name PH1, id 503 from chain A The Residue name PH1, id 504 from chain A The Residue name PH1, id 505 from chain A The Residue name PH1, id 506 from chain A The Residue name PH1, id 507 from chain A The Residue name PH1, id 508 from chain A The Residue name HOH, id 405 from chain A The Residue name HOH, id 410 from chain A The Residue name HOH, id 412 from chain A The Residue name HOH, id 414 from chain A The Residue name HOH, id 424 from chain A The Residue name HOH, id 425 from chain A The Residue name HOH, id 427 from chain A The Residue name HOH, id 431 from chain A The Residue name HOH, id 432 from chain A The Residue name HOH, id 433 from chain A The Residue name HOH, id 437 from chain A The Residue name HOH, id 438 from chain A The Residue name HOH, id 439 from chain A The Residue name HOH, id 441 from chain A The Residue name HOH, id 442 from chain A The Residue name HOH, id 443 from chain A The Residue name HOH, id 444 from chain A The following residues were renamed: The Residue name LYS, id 216 from chain A renamed as LYR The Residue name , id 300 from chain A renamed as LYR The Residue name LYS, id 216 from chain A renamed as LYR The following atoms were renamed: Atom from Residue ID 216, residue name LYR, chain A, originally name NZ was renamed as N16 The following residues were reorder: The Residue ID 300, residue name LYR, chain A, originally ID 300 was reorder to the ID 216 ================================================================================= ================================== MD Protocols ==================================== The structure 1qhj_vacuum.psf was prepared using VMD[1] and the plugin QwikMD[2]. The MD simulations in the present study were performed employing the NAMD molecular dynamics package[3]. The CHARMM36 force field[4,5] was used in all MD simulaitons. The Minimization was performed with no solvent representation model, simulation performed in vacuum, applying a dielectric constant of 80.0. A distance cut-off of 16.0 Å was applied to short-range, non-bonded interactions, and 15.0 Å for the smothering functions. Before the MD simulations all the systems were submitted to an energy minimization protocol for 2000 steps. The Annealing was performed with no solvent representation model, simulation performed in vacuum, applying a dielectric constant of 80.0. A temperature ramp was performed consisted of 0.24 ns of simulation where the temperature was raised from 60 K to 300 K A distance cut-off of 16.0 Å was applied to short-range, non-bonded interactions, and 15.0 Å for the smothering functions. The equations of motion were integrated using the r-RESPA multiple time step scheme[3] to update the short-range interactions every 1 steps and long-range electrostatics interactions every 2 steps. The time step of integration was chosen to be 2 fs for all simulations.In this step consisted of 0.29 ns of simulation, the atoms defined by the selection "backbone" were restrained. The Equilibration was performed with no solvent representation model, simulation performed in vacuum, applying a dielectric constant of 80.0. The temperature was maintained at 300 K using Langevin dynamics. A distance cut-off of 16.0 Å was applied to short-range, non-bonded interactions, and 15.0 Å for the smothering functions. The equations of motion were integrated using the r-RESPA multiple time step scheme[3] to update the short-range interactions every 1 steps and long-range electrostatics interactions every 2 steps. The time step of integration was chosen to be 2 fs for all simulations.In this step consisted of 1.00 ns of simulation, the atoms defined by the selection "backbone" were restrained. The MD was performed with no solvent representation model, simulation performed in vacuum, applying a dielectric constant of 80.0. The temperature was maintained at 300 K using Langevin dynamics. A distance cut-off of 16.0 Å was applied to short-range, non-bonded interactions, and 15.0 Å for the smothering functions. The equations of motion were integrated using the r-RESPA multiple time step scheme[3] to update the short-range interactions every 1 steps and long-range electrostatics interactions every 2 steps. The time step of integration was chosen to be 2 fs for all simulations.In this step consisted of 5.00 ns of simulation, no atoms were constrained. The MD.1 was performed with no solvent representation model, simulation performed in vacuum, applying a dielectric constant of 80.0. The temperature was maintained at 300 K using Langevin dynamics. A distance cut-off of 16 Å was applied to short-range, non-bonded interactions, and 15 Å for the smothering functions. The equations of motion were integrated using the r-RESPA multiple time step scheme[3] to update the short-range interactions every 1 steps and long-range electrostatics interactions every 2 steps. The time step of integration was chosen to be 2 fs for all simulations.In this step consisted of 5.00 ns of simulation, no atoms were constrained. Bibliography: {1} Humphrey, W., Dalke, A. and Schulten, K., "VMD - Visual Molecular Dynamics", J. Molec. Graphics, 1996, vol. 14, pp. 33-38. {2} Ribeiro, J. V., Bernardi, R. C., Rudack, T., Stone, J. E., Phillips J. C., Freddolino P. L. and Schulten, K.,"QwikMD-integrative molecular dynamics toolkit for novices and experts", Sci. Rep., 2016 {3} Phillips J. C., Braun, R. , Wang, W., Gumbart, J. , Tajkhorshid, E., Villa, E. , Chipot, C. , Skeel, R. D., Kale, L., and Schulten, K., "Scalable molecular dynamics with NAMD", J. Comp. Chem, 2005, vol 26, pp. 1781-1802 {4} Best, R. B., Zhu, X., Shim, J., Lopes, P. E. M., Mittal, J., Feig, M. and MacKerell, A. D., "Optimization of the additive CHARMM All-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ 1and χ 2dihedral Angles", J. Chem. Theory Comput.,2012, vol. 8, pp. 3257–3273. {5} MacKerell, A. D., Jr., Bashford, D., Bellott, M., R. L. , Jr., Evanseck, J. D., Field, M. J., Fischer, S., Gao J., Guo, H., Ha S., Joseph-McCarthy, D., Kuchnir, L., Kuczera, K., Lau, F. T. K., Mattos, C., Michnick. S., Ngo, T., Nguyen, D. T., Prodhom, B., Reiher, W. E., Roux, B., Schlenkrich, M., Smith, J. C., Stote, R., Straub, J., Watanabe, M., Wiórkiewicz-Kuczera, J., Yin, D. and Karplus M., "All-atom empirical potential for molecular modeling and dynamics studies of proteins", J. Phys. Chem. B, 1998 , vol. 102, pp. 3586-3616 ================================================================================= ================================== MD Analysis ==================================== The initial structure 1qhj_vacuum_QwikMD.pdb was loaded. The following structure/trajectories were loaded: Minimization; Annealing; Equilibration; MD; MD.1; The trajectories were loaded every 1 frames. The initial structure 1qhj_vacuum_QwikMD.pdb was loaded. The following structure/trajectories were loaded: Minimization; Annealing; Equilibration; MD; MD.1; The trajectories were loaded every 1 frames. The Root-Mean-Square Deviation (RMSD) was calculated over 572 frames corresponding to a total of 10.57 ns. The trajectory frames were aligned against the atom selection "backbone" of the first frame. The RMSD was calculated for the atom selection "backbone". The initial structure 1qhj_vacuum_QwikMD.pdb was loaded. The following structure/trajectories were loaded: Minimization; Annealing; Equilibration; MD; MD.1; The trajectories were loaded every 1 frames. The Root-Mean-Square Deviation (RMSD) was calculated over 572 frames corresponding to a total of 10.57 ns. The trajectory frames were aligned against the atom selection "backbone" of the first frame. The RMSD was calculated for the atom selection "backbone". The initial structure 1qhj_vacuum_QwikMD.pdb was loaded. The following structure/trajectories were loaded: Minimization; Annealing; Equilibration; MD; MD.1; The trajectories were loaded every 1 frames. The Root-Mean-Square Deviation (RMSD) was calculated over 572 frames corresponding to a total of 10.57 ns. The trajectory frames were aligned against the atom selection "backbone" of the first frame. The RMSD was calculated for the atom selection "backbone". The following structure/trajectories were loaded: Equilibration; The trajectories were loaded every 1 frames. The Root-Mean-Square Deviation (RMSD) was calculated over 25 frames corresponding to a total of 0.48 ns. The trajectory frames were aligned against the atom selection "backbone" of the first frame. The RMSD was calculated for the atom selection "backbone". The following structure/trajectories were loaded: Equilibration; The trajectories were loaded every 1 frames. The Root-Mean-Square Deviation (RMSD) was calculated over 25 frames corresponding to a total of 0.48 ns. The trajectory frames were aligned against the atom selection "backbone" of the first frame. The RMSD was calculated for the atom selection "backbone". The following structure/trajectories were loaded: Equilibration; The trajectories were loaded every 1 frames. The Root-Mean-Square Deviation (RMSD) was calculated over 25 frames corresponding to a total of 0.48 ns. The trajectory frames were aligned against the atom selection "backbone" of the first frame. The RMSD was calculated for the atom selection "backbone". The following structure/trajectories were loaded: Equilibration; The trajectories were loaded every 1 frames. The following structure/trajectories were loaded: Equilibration; The trajectories were loaded every 1 frames. The Root-Mean-Square Deviation (RMSD) was calculated over 25 frames corresponding to a total of 0.48 ns. The trajectory frames were aligned against the atom selection "backbone" of the first frame. The RMSD was calculated for the atom selection "backbone". The following structure/trajectories were loaded: Annealing; The trajectories were loaded every 1 frames. The Root-Mean-Square Deviation (RMSD) was calculated over 44 frames corresponding to a total of 0.09 ns. The trajectory frames were aligned against the atom selection "backbone" of the first frame. The RMSD was calculated for the atom selection "backbone". The energies were evaluated over time for 0.31 ns every (0.00080 ns (400 steps), on a running average of 0.00120 ns (600 steps) average length (the energies output frequency was 40 steps or 0.00008 ns). The energies evaluated were: kinetic. The energies were evaluated over time for 0.31 ns every (0.00080 ns (400 steps), on a running average of 0.00120 ns (600 steps) average length (the energies output frequency was 40 steps or 0.00008 ns). The energies evaluated were: potential. The initial structure 1qhj_vacuum_QwikMD.pdb was loaded. The following structure/trajectories were loaded: MD; MD.1; The trajectories were loaded every 1 frames. The Root-Mean-Square Deviation (RMSD) was calculated over 501 frames corresponding to a total of 10.00 ns. The trajectory frames were aligned against the atom selection "backbone" of the first frame. The RMSD was calculated for the atom selection "backbone". The initial structure 1qhj_vacuum_QwikMD.pdb was loaded. The following structure/trajectories were loaded: Equilibration; The trajectories were loaded every 1 frames. The Root-Mean-Square Deviation (RMSD) was calculated over 26 frames corresponding to a total of 0.50 ns. The trajectory frames were aligned against the atom selection "backbone" of the first frame. The RMSD was calculated for the atom selection "backbone". The initial structure 1qhj_vacuum_QwikMD.pdb was loaded. The following structure/trajectories were loaded: Minimization; Annealing; Equilibration; The trajectories were loaded every 1 frames. The Root-Mean-Square Deviation (RMSD) was calculated over 72 frames corresponding to a total of 0.57 ns. The trajectory frames were aligned against the atom selection "backbone" of the first frame. The RMSD was calculated for the atom selection "backbone". The initial structure 1qhj_vacuum_QwikMD.pdb was loaded. The following structure/trajectories were loaded: Equilibration; The trajectories were loaded every 1 frames. The Root-Mean-Square Deviation (RMSD) was calculated over 26 frames corresponding to a total of 0.50 ns. The trajectory frames were aligned against the atom selection "backbone" of the first frame. The RMSD was calculated for the atom selection "backbone".