Coarse-Grained Two-State Stochastic Dynamics on a Reference Bead Configuration¶
- Task ID:
biology.protein_folding_go_model - Domain:
biology - Subdomain:
biophysics - Status:
test - Tags:
langevin,multi_temperature,free_energy,heat_capacity,coarse_grained,stochastic_dynamics
Public Summary¶
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Example B1 Prompt Excerpt¶
# B1: Coarse-Grained Two-State Folding of a Reference Bead Configuration (Gō Model)
## Background
You are given a small reference bead configuration — 20 points in 3D — that plays the role of a **native structure** in a **Cα-only Gō-type coarse-grained model** of a miniprotein (conceptually Trp-cage, PDB 1L2Y). The goal is to
1. run **multi-temperature Langevin dynamics** in this potential,
2. reconstruct the **free-energy landscape** along the native-contact order parameter
$Q$ = fraction of reference contacts that are formed,
3. locate the **folding temperature** $T_f$ (specific-heat peak / $\langle Q\rangle(T)$ midpoint),
4. show that the distribution $P(Q)$ at $T_f$ is (weakly) **bimodal** and report the
Notes¶
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