File generated by QwikMD (version 1.1) on 11:43-CDT, 10/05/2016 Machine name: maseru.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 1kjf was loaded directly from PDB website. The original structure can be found at /Scr/scr-test-jribeiro/qwimd_tutorial_simulaitons/1kjf/HIVprotease_without_substrate/setup/1kjf_original.pdb The atom selection defined by the following pairs chain&type were deleted: P and protein The following residues were renamed: The Residue name ACT, id 504 from chain A renamed as ACET The Residue name ACT, id 501 from chain B renamed as ACET The Residue name ACT, id 502 from chain B renamed as ACET The Residue name ACT, id 503 from chain B renamed as ACET The following atoms were renamed: Atom from Residue ID 504, residue name ACET, chain A, originally name C was renamed as C2 Atom from Residue ID 501, residue name ACET, chain B, originally name C was renamed as C2 Atom from Residue ID 502, residue name ACET, chain B, originally name C was renamed as C2 Atom from Residue ID 503, residue name ACET, chain B, originally name C was renamed as C2 Atom from Residue ID 504, residue name ACET, chain A, originally name O was renamed as O1 Atom from Residue ID 501, residue name ACET, chain B, originally name O was renamed as O1 Atom from Residue ID 502, residue name ACET, chain B, originally name O was renamed as O1 Atom from Residue ID 503, residue name ACET, chain B, originally name O was renamed as O1 Atom from Residue ID 504, residue name ACET, chain A, originally name OXT was renamed as O2 Atom from Residue ID 501, residue name ACET, chain B, originally name OXT was renamed as O2 Atom from Residue ID 502, residue name ACET, chain B, originally name OXT was renamed as O2 Atom from Residue ID 503, residue name ACET, chain B, originally name OXT was renamed as O2 Atom from Residue ID 504, residue name ACET, chain A, originally name CH3 was renamed as C1 Atom from Residue ID 501, residue name ACET, chain B, originally name CH3 was renamed as C1 Atom from Residue ID 502, residue name ACET, chain B, originally name CH3 was renamed as C1 Atom from Residue ID 503, residue name ACET, chain B, originally name CH3 was renamed as C1 The system was solvated a using water box with a 20 Å buffer a water box of the dimensions 98.88,80.69,76.34 (x,y,z in Å) placed at (-51.36,-41.12,-37.68) and (47.52,39.58,38.66) as minimum and maximum coordinates. The molecule was also rotated to minimize the solvent box volume. A total of 17985 water molecules TIP3[1] model were placed. After the addition of the water molecules, the system presented a total net charge of 4.000. The system was neutralized and in total 55 CLA ions plus 51 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 was performed with explicit solvent using the TIP3 water model[1] in the NpT ensemble. 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)[7] method. Before the MD simulations all the systems were submitted to an energy minimization protocol for 2000 steps. The Annealing 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 K The pressure was maintained at 1 atm usign Nosé-Hoover Langevin piston[8,9]. 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)[7] 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 0.29 ns of simulation, the atoms defined by the selection "backbone" were restrained. The Equilibration was performed with explicit solvent using the TIP3 water model[1] in the NpT ensemble. The temperature was maintained at 300 K using Langevin dynamics. The pressure was maintained at 1 atm usign Nosé-Hoover Langevin piston[8,9]. 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)[7] 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 1.00 ns of simulation, the atoms defined by the selection "backbone" were restrained. The MD was performed with explicit solvent using the TIP3 water model[1] in the NpT ensemble. The temperature was maintained at 300 K using Langevin dynamics. The pressure was maintained at 1 atm usign Nosé-Hoover Langevin piston[8,9]. 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)[7] 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 2.00 ns of simulation, no atoms were constrained. The MD.1 was performed with explicit solvent using the TIP3 water model[1] in the NpT ensemble. The temperature was maintained at 300 K using Langevin dynamics. 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)[7] 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 2.00 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} 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 {8} Martyna, G. J., Tobias, D. J. and Klein, M. L., "Constant pressure molecular dynamics algorithms", J. Chem. Phys., 1994, vol. 101 {9} 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 ================================================================================= ================================== MD Analysis ==================================== The initial structure HIVprotease_without_substrate_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 2504 frames corresponding to a total of 25.03 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 HIVprotease_without_substrate_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 2588 frames corresponding to a total of 25.87 ns. The trajectory frames were aligned against the atom selection "(chain A B) and not resid 35 to 57" of the first frame. The RMSD was calculated for the atom selection "(chain A B) and resid 35 to 57". The Root-Mean-Square Deviation (RMSD) was calculated over 2588 frames corresponding to a total of 25.87 ns. The trajectory frames were aligned against the atom selection "backbone" of the first frame. The RMSD was calculated for the atom selection "(chain A B) and resid 35 to 57". The initial structure HIVprotease_without_substrate_QwikMD_nowater_noions.pdb was loaded. The following structure/trajectories were loaded: Minimization; Annealing; Equilibration; MD; MD.1; The trajectories were loaded every 1 frames. The water molecules, solvent ion molecules were not included in the loading process. The Root-Mean-Square Deviation (RMSD) was calculated over 4247 frames corresponding to a total of 41.28 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 HIVprotease_without_substrate_QwikMD.pdb was loaded. The following structure/trajectories were loaded: Minimization; Annealing; Equilibration; MD; MD.1; The trajectories were loaded every 1 frames. The energies were evaluated over time for 41.32 ns every (0.02000 ns (10000 steps), on a running average of 0.03000 ns (15000 steps) average length (the energies output frequency was 1000 steps or 0.00200 ns). The energies evaluated were: total.