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the problem about equilibration trajectories in IFP_generation_examples_TRAJ.ipynb scripts section 2.2 #11

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tanshy17 opened this issue Nov 9, 2022 · 0 comments

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@tanshy17
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tanshy17 commented Nov 9, 2022

Hello~
Thank you for developing tau RAMD analysis, and contributing code.
I have followed your RAMD tutorial (https://kbbox.h-its.org/toolbox/tutorials/estimation-of-relative-residence-times-of-protein-ligand-complexes-using-random-acceleration-molecular-dynamics-ramd-implementation-in-namd/) to get the dissociation trajectory. And I want to analysis using this code. I have a problem about equilibration trajectories in IFP_generation_examples_TRAJ.ipynb scripts section 2.2. What equilibration trajectories should I use? Can I use the equilibration trajectories by amber in step3, or amber2namd_equilibr.dcd in the step4(https://kbbox.h-its.org/toolbox/tutorials/estimation-of-relative-residence-times-of-protein-ligand-complexes-using-random-acceleration-molecular-dynamics-ramd-implementation-in-namd/) , or both them are ok?
Looking forward your reply!
Thanks in advance!

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