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pablo-arantes / making-it-rain

Cloud-based molecular simulations for everyone
MIT License
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Continuing trajectory analysis from previous MD simulation #106

Open tegarachsendo opened 5 months ago

tegarachsendo commented 5 months ago

Hi. First of all i'd like to say thank you very much for providing this notebook so that i can perform fast high throughput MD simulation in just less than a month.

My question is how can we continue performing various trajectory analysis without having to come back to square one (redo the simulation). From what i understand, it appears that there are some kind of simplification (not quite sure though) in the early part of code so that when i started in the middle or near end (e.g. concatenation of trajectory), it gave error. I am not quite understand how python language is so i have difficulties in copying command to add to trajectory analysis to make it work.

So far i have extract RMSD and RMSF data and i would like to do mmPBSA analysis and radius of gyration analysis. Thank you for your kind help

Regards

tegarachsendo commented 5 months ago

Notes: I have performed the simulation previously but want to continue processing the trajectory in the following day after the notebook is disconnected.