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This repository contains codes to construct many-body coarse grained molecular model of chignolin, including 2-body, 2,3-body, 2,3,4-body, 2,3,4C-body, and 2,3,4C,5-body, where 'C' represent chiral.
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Since the implementation of differemnt order of many-body required different codes, different many-body models are in different sub folders.
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In each many-body models, there are 4 individual procedures:
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1_CV: conduct cross-validation, and traning of the model.
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2_Simulation: conduct coarse graining simulation using the trained model.
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3_FE: compute free energy of the simulation trajectory on 2-dimensional TICA space.
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4_Potential_Decomp: calculate the CG potential predicted by many-body models.
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The original all-atom trajecotry of Chignolin for training the CG model can be accessed through the link: https://figshare.com/articles/dataset/Chignolin_Simulations/13858898