File generated by QwikMD (version 1.1) on 12:38-CDT, 10/01/2016 Machine name: joao-mac-ks.local (MacOS). ============================================================================== 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 1ubq was loaded directly from PDB website. The original structure can be found at /Users/joaoribeiro/Desktop/MD_for_highlights/Ubiquitin/setup/1ubq_original.pdb The system was solvated a using cubic water box with a 7.5 Å buffer additionally to the system longest dimension a water box of the dimensions 75.59,75.59,75.59 (x,y,z in Å) placed at (-37.42,-36.42,-35.73) and (38.17,39.17,39.86) as minimum and maximum coordinates. A total of 13098 water molecules TIP3[1] model were placed. After the addition of the water molecules, the system presented a total net charge of 0.000. 37 CLA ions plus 37 SOD ions were added to the system making up a salt concentration of 0.15 mol/L. ================================================================================= ================================== MD Protocols ==================================== The structure ionized.psf was prepared using VMD[2] and the plugin QwikMD[3]. The MD simulations in the present study were performed employing the NAMD molecular dynamics package[4]. The CHARMM36 force field[5,6] was used in all MD simulaitons. The Minimization and Constrained equilibration MD Simulation was performed with explicit solvent using the TIP3 water model[1] in the NpT ensemble. A temperature ramp was performed consisted of 0.24 ns of simulation where the temperature was raised from 60 K to 300.00 K The pressure was maintained at 1 atm usign Nosé-Hoover Langevin piston[7,8]. A distance cut-off of 12.0 Å was applied to short-range, non-bonded interactions, and 10.0 Å for the smothering functions. Long-range electrostatic interactions were treated using the particle-mesh Ewald (PME)[9] method. The equations of motion were integrated using the r-RESPA multiple time step scheme[4] 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. Before the MD simulations all the systems were submitted to an energy minimization protocol for 1000 steps. In this step consisted of 1.00 ns of simulation, the atoms defined by the selection "protein and backbone" were restrained. The MD Simulation without constrains was performed with explicit solvent using the TIP3 water model[1] in the NpT ensemble. The temperature was maintained at 300.00 K using Langevin dynamics. The pressure was maintained at 1 atm usign Nosé-Hoover Langevin piston[7,8]. A distance cut-off of 12.0 Å was applied to short-range, non-bonded interactions, and 10.0 Å for the smothering functions. Long-range electrostatic interactions were treated using the particle-mesh Ewald (PME)[9] method. The equations of motion were integrated using the r-RESPA multiple time step scheme[4] 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 5.0 ns of simulation, no atoms were constrained. Bibliography: {1} Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W. and Klein, M. L., "Comparison of simple potential functions for simulating liquid water", J. Chem. Phys., 1983, vol 79, 6127-6129. {2} Humphrey, W., Dalke, A. and Schulten, K., "VMD - Visual Molecular Dynamics", J. Molec. Graphics, 1996, vol. 14, pp. 33-38. {3} 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 {4} 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 {5} 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. {6} 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 {7} Martyna, G. J., Tobias, D. J. and Klein, M. L., "Constant pressure molecular dynamics algorithms", J. Chem. Phys., 1994, vol. 101 {8} Feller, S. E., Zhang, Y., Pastor, R. W. and Brooks, B.R., "Constant pressure molecular dynamics simulation: The Langevin piston method", J. Chem. Phys., 1995, vol. 103 {9} Darden, T., York, D. & Pedersen and L., "Particle mesh Ewald: An Nlog(N) method for Ewald sums in large systems", J. Chem. Phys., 1993, vol. 98, pp. 10089-10092 ================================================================================= ================================== MD Analysis ==================================== The initial structure Ubiquitin_QwikMD_nowater_noions.pdb was loaded. The following structure/trajectories were loaded: qwikmd_equilibration_0; qwikmd_production_1; The trajectories were loaded every 1 frames. The water molecules, solvent ion molecules were not included in the loading process. The initial structure Ubiquitin_QwikMD.pdb was loaded. The following structure/trajectories were loaded: qwikmd_equilibration_0; qwikmd_production_1; The trajectories were loaded every 1 frames. The Root-Mean-Square Deviation (RMSD) was calculated over 313 frames corresponding to a total of 6.24 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 Ubiquitin_QwikMD.pdb was loaded. The following structure/trajectories were loaded: qwikmd_production_1; The trajectories were loaded every 1 frames. The Root-Mean-Square Deviation (RMSD) was calculated over 251 frames corresponding to a total of 5.00 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 Ubiquitin_QwikMD.pdb was loaded. The following structure/trajectories were loaded: qwikmd_equilibration_0; qwikmd_production_1; The trajectories were loaded every 1 frames. The Root-Mean-Square Deviation (RMSD) was calculated over 313 frames corresponding to a total of 6.24 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 thermodynamic properties were evaluated over time for 6.29 ns every (0.00800 ns (4000 steps), on a running average of 0.01200 ns (6000 steps) average length (the energies output frequency was 400 steps or 0.00080 ns). The properties evaluated were: temperature; pressure; volume. The initial structure Ubiquitin_QwikMD.pdb was loaded. The following structure/trajectories were loaded: qwikmd_equilibration_0; The trajectories were loaded every 1 frames. The thermodynamic properties were evaluated over time for 0.00 ns every (0.00800 ns (4000 steps), on a running average of 0.01200 ns (6000 steps) average length (the energies output frequency was 400 steps or 0.00080 ns). The properties evaluated were: temperature. The thermodynamic properties were evaluated over time for 0.00 ns every (0.00800 ns (4000 steps), on a running average of 0.01200 ns (6000 steps) average length (the energies output frequency was 400 steps or 0.00080 ns). The properties evaluated were: pressure. The initial structure Ubiquitin_QwikMD.pdb was loaded. The following structure/trajectories were loaded: qwikmd_equilibration_0; The trajectories were loaded every 1 frames. The thermodynamic properties were evaluated over time for 0.00 ns every (0.00800 ns (4000 steps), on a running average of 0.01200 ns (6000 steps) average length (the energies output frequency was 400 steps or 0.00080 ns). The properties evaluated were: temperature. The initial structure Ubiquitin_QwikMD.pdb was loaded. The following structure/trajectories were loaded: qwikmd_equilibration_0; The trajectories were loaded every 1 frames. The thermodynamic properties were evaluated over time for 0.00 ns every (0.00800 ns (4000 steps), on a running average of 0.01200 ns (6000 steps) average length (the energies output frequency was 400 steps or 0.00080 ns). The properties evaluated were: temperature. The initial structure Ubiquitin_QwikMD.pdb was loaded. The following structure/trajectories were loaded: qwikmd_equilibration_0; The trajectories were loaded every 1 frames. The thermodynamic properties were evaluated over time for 0.00 ns every (0.00800 ns (4000 steps), on a running average of 0.01200 ns (6000 steps) average length (the energies output frequency was 400 steps or 0.00080 ns). The properties evaluated were: temperature. The initial structure Ubiquitin_QwikMD.pdb was loaded. The following structure/trajectories were loaded: qwikmd_equilibration_0; The trajectories were loaded every 1 frames. The thermodynamic properties were evaluated over time for 0.00 ns every (0.00800 ns (4000 steps), on a running average of 0.01200 ns (6000 steps) average length (the energies output frequency was 400 steps or 0.00080 ns). The properties evaluated were: temperature. The initial structure Ubiquitin_QwikMD.pdb was loaded. The following structure/trajectories were loaded: qwikmd_equilibration_0; The trajectories were loaded every 1 frames. The energies were evaluated over time for 0.01 ns every (0.00002 ns (10 steps), on a running average of 0.00003 ns (15 steps) average length (the energies output frequency was 1 steps or 0.00000 ns). The energies evaluated were: total. The initial structure Ubiquitin_QwikMD.pdb was loaded. The following structure/trajectories were loaded: qwikmd_equilibration_0; The trajectories were loaded every 1 frames. The thermodynamic properties were evaluated over time for 0.01 ns every (0.00002 ns (10 steps), on a running average of 0.00003 ns (15 steps) average length (the energies output frequency was 1 steps or 0.00000 ns). The properties evaluated were: temperature. The initial structure Ubiquitin_QwikMD.pdb was loaded. The following structure/trajectories were loaded: qwikmd_equilibration_0; The trajectories were loaded every 1 frames. The thermodynamic properties were evaluated over time for 0.01 ns every (0.00002 ns (10 steps), on a running average of 0.00003 ns (15 steps) average length (the energies output frequency was 1 steps or 0.00000 ns). The properties evaluated were: temperature. The initial structure Ubiquitin_QwikMD.pdb was loaded. The following structure/trajectories were loaded: qwikmd_equilibration_0; The trajectories were loaded every 1 frames. The thermodynamic properties were evaluated over time for 0.01 ns every (0.00002 ns (10 steps), on a running average of 0.00003 ns (15 steps) average length (the energies output frequency was 1 steps or 0.00000 ns). The properties evaluated were: temperature. The initial structure Ubiquitin_QwikMD.pdb was loaded. The following structure/trajectories were loaded: qwikmd_equilibration_0; The trajectories were loaded every 1 frames. The thermodynamic properties were evaluated over time for 1.29 ns every (0.00800 ns (4000 steps), on a running average of 0.01200 ns (6000 steps) average length (the energies output frequency was 400 steps or 0.00080 ns). The properties evaluated were: temperature. The energies were evaluated over time for 1.29 ns every (0.00800 ns (4000 steps), on a running average of 0.01200 ns (6000 steps) average length (the energies output frequency was 400 steps or 0.00080 ns). The energies evaluated were: total; kinetic. The thermodynamic properties were evaluated over time for 1.29 ns every (0.00800 ns (4000 steps), on a running average of 0.01200 ns (6000 steps) average length (the energies output frequency was 400 steps or 0.00080 ns). The properties evaluated were: pressure. The initial structure Ubiquitin_QwikMD.pdb was loaded. The following structure/trajectories were loaded: qwikmd_equilibration_0; qwikmd_production_1; The trajectories were loaded every 1 frames. The thermodynamic properties were evaluated over time for 6.29 ns every (0.00800 ns (4000 steps), on a running average of 0.01200 ns (6000 steps) average length (the energies output frequency was 400 steps or 0.00080 ns). The properties evaluated were: temperature. The initial structure Ubiquitin_QwikMD.pdb was loaded. The following structure/trajectories were loaded: qwikmd_production_1; The trajectories were loaded every 1 frames. The thermodynamic properties were evaluated over time for 5.00 ns every (0.00800 ns (4000 steps), on a running average of 0.01200 ns (6000 steps) average length (the energies output frequency was 400 steps or 0.00080 ns). The properties evaluated were: temperature. The initial structure Ubiquitin_QwikMD.pdb was loaded. The following structure/trajectories were loaded: qwikmd_equilibration_0; The trajectories were loaded every 1 frames. The thermodynamic properties were evaluated over time for 1.29 ns every (0.00800 ns (4000 steps), on a running average of 0.01200 ns (6000 steps) average length (the energies output frequency was 400 steps or 0.00080 ns). The properties evaluated were: temperature. The energies were evaluated over time for 1.29 ns every (0.00800 ns (4000 steps), on a running average of 0.01200 ns (6000 steps) average length (the energies output frequency was 400 steps or 0.00080 ns). The energies evaluated were: total. The initial structure Ubiquitin_QwikMD.pdb was loaded. The following structure/trajectories were loaded: qwikmd_equilibration_0; qwikmd_production_1; The trajectories were loaded every 1 frames. The energies were evaluated over time for 6.29 ns every (0.00800 ns (4000 steps), on a running average of 0.01200 ns (6000 steps) average length (the energies output frequency was 400 steps or 0.00080 ns). The energies evaluated were: kinetic; potential. The energies were evaluated over time for 6.29 ns every (0.00800 ns (4000 steps), on a running average of 0.01200 ns (6000 steps) average length (the energies output frequency was 400 steps or 0.00080 ns). The energies evaluated were: total. The Root-Mean-Square Deviation (RMSD) was calculated over 313 frames corresponding to a total of 6.24 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 thermodynamic properties were evaluated over time for 6.29 ns every (0.00800 ns (4000 steps), on a running average of 0.01200 ns (6000 steps) average length (the energies output frequency was 400 steps or 0.00080 ns). The properties evaluated were: temperature; pressure; volume.