File generated by QwikMD (version 1.1) on 15:07-CDT, 10/07/2016 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 smd_ini.pdb was loaded from a local folder: /Scr/scr-test-jribeiro/qwimd_tutorial_simulaitons/SMD/files. The original structure can be found at /Scr/scr-test-jribeiro/qwimd_tutorial_simulaitons/SMD/files/Deca-alanine/setup/smd_ini_original.pdb ================================================================================= ================================== MD Protocols ==================================== The structure Deca-alanine.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 SMD simulation was performed with implicit solvent represented by the Generalized Born/solvent-accessible surface area model[6,7,8]. The temperature was maintained at 300.00 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.The SMD simulations[9] of constant velocity stretching (SMD-CV protocol) employing a pulling speed of 1 Å/ns and a harmonic constraint force of 7.0 kcal/mol/Å^2 was performed for 20.0 ns. In this step, SMD was employed by harmonically restraining the position of ALA10B residues, and moving a second restraint residues ALA1B, with constant velocity in the axis defined by the two group of restrained residues. 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 {6} Still, W. C., Tempczyk, A., Hawley, R. C.; Hendrickson, T., "Semianalytical treatment of solvation for molecular mechanics and dynamics", J. Am. Chem. Soc., 1990, vol. 112, pp. 3257-3273. {7} Tanner, D. E., Phillips J. C. and Schulten, K., "GPU/CPU Algorithm for Generalized Born/Solvent-Accessible Surface Area Implicit Solvent Calculations", J. Phys. Chem. B,1998 , vol. 102, pp. 3586-3616 {8} Tanner, D. E., Chan, K. , Phillips J. C. and Schulten, K., "Parallel generalized Born implicit solvent calculations with NAMD.", J. Chem. Theor. Comp., 2011 , vol. 7, pp. 3635-3642 {9} Izrailev, S., Stepaniants, S., Balsera, M., Oono, Y. and Schulten, K.,"Molecular dynamics study of unbinding of the avidin-biotin complex", Biophys. J., 1997, vol 72, pp. 1568–1581 ================================================================================= ================================== MD Analysis ==================================== The initial structure Deca-alanine_QwikMD.pdb was loaded. The following structure/trajectories were loaded: qwikmd_production_smd_0; The trajectories were loaded every 1 frames. The initial structure Deca-alanine_QwikMD.pdb was loaded. The following structure/trajectories were loaded: qwikmd_production_smd_0; The trajectories were loaded every 1 frames. The initial structure Deca-alanine_QwikMD.pdb was loaded. The following structure/trajectories were loaded: qwikmd_production_smd_0; The trajectories were loaded every 1 frames. The Root-Mean-Square Deviation (RMSD) was calculated over 1001 frames corresponding to a total of 20.00 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 energies were evaluated over time for 20.00 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 energies evaluated were: kinetic; potential.