"EXPLORATION OF THE NUCLEATION PATHWAY FOR SUPRAMOLECULAR FIBERS"

Authors: Tang, Phu; Khatua, Prabir; Carnevale, Vincenzo; Loverde, Sharon

Topology

System CPT-Only: cpt_24.prmtop

System I, II, III have the same initial configuration: tt1_12mol_cubic.prmtop

Production run

Conventional MD: production_conventional_MD.in

Metadynamics MD: production_METAD.in

Analysis

STEP 1: Calculating Stacking Index

STEP 2: Combining data from PLUMED outputs and calculated stacking index from STEP 1

STEP 3: Calculating and visualizing the free energy profiles

Miscellaneous

find-frame.py will extract frames with chosen parameters (sl, si, ac, or k2).