Updated workflow#2
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Trajectories preparation: Step1.Run XYZtraj-Trajs.py Processing on the initial trajectories from Progdyn simulation 1.Previous ntraj file is the trajectories after processing. Updated ntraj file is the initial trajectories from Progdyn simulation. 2.Add procedure files: ./Trajectories preparation/Processing/reorder, TDD, TDD_p2p, TDD_r2pA, TDD_r2pB, TDD_r2r, trajTS 3.Update script : XYZtraj-Trajs_QZX.py 4.Update script : traj.conf
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Run truncation.py 1.Trajectories of product A and B should be treated separately. 2.Update Truncation_QZ.py
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1.Trajectories of product A and B should be treated separately. 2.Update Subsection_QZ.py 3.Update new range of bond(4,14) length file--bond(4,14).xlsx based on the average interval bond length.
Update procedure files during the topology file preparation:
1.Delete entropy_anal.py. When analyzing output result, just need the total configuration entropy in MIST.txt file and don't need to use extra script to obtain data. 2.Trajectories of product A and B should be treated separately. 3.Add output_analysis.xlsx file and the unit conversion method is labeled in Excle file.
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Trajectories preparation:
Step1.Run XYZtraj-Trajs.py
Processing on the initial trajectories from Progdyn simulation
1.Previous ntraj file is the trajectories after processing. Updated ntraj file is the initial trajectories from Progdyn simulation.
2.Add procedure files during running the XYZtraj-Trajs.py: ./Trajectories preparation/Processing/reorder, TDD, TDD_p2p, TDD_r2pA, TDD_r2pB, TDD_r2r, trajTS
3.Update script : XYZtraj-Trajs_QZX.py
4.Update script : traj.conf