Public
- Public
- Groups
- Popular
- People

Conversation

Notices

arXiv Quantitative Biology (arxivbio@qoto.org)'s status on Friday, 13-Dec-2019 03:25:06 UTC arXiv Quantitative Biology

Adaptive Markov State Model estimation using short reseeding trajectories. (arXiv:1912.05724v1 [q-bio.BM]) http://arxiv.org/abs/1912.05724
In conversation Friday, 13-Dec-2019 03:25:06 UTC from qoto.org permalink
Attachments
1. Adaptive Markov State Model estimation using short reseeding trajectories
  
  In the last decade, advances in molecular dynamics (MD) and Markov State Model (MSM) methodologies have made possible accurate and efficient estimation of kinetic rates and reactive pathways for complex biomolecular dynamics occurring on slow timescales. A promising approach to enhanced sampling of MSMs is to use so-called "adaptive" methods, in which new MD trajectories are "seeded" preferentially from previously identified states. Here, we investigate the performance of various MSM estimators applied to reseeding trajectory data, for both a simple 1D free energy landscape, and for mini-protein folding MSMs of WW domain and NTL9(1-39). Our results reveal the practical challenges of reseeding simulations, and suggest a simple way to reweight seeding trajectory data to better estimate both thermodynamic and kinetic quantities.
- 🎓 Dr. Freemo :jpf: 🇳🇱 repeated this.

Feeds