Refine
Year of publication
- 2013 (15) (remove)
Document Type
- Article (9)
- ZIB-Report (4)
- Other (2)
Is part of the Bibliography
- no (15)
Keywords
- Markov State Models (2)
- Conformation Dynamics (1)
- Markov chains (1)
- Meshfree (1)
- Molecular Kinetics (1)
- Molecular Simulation (1)
- Partition of Unity (1)
- Perron Frobenius Generalization (1)
- Pre Kernel (1)
- Rebinding (1)
Institute
A hands-off linear interaction energy approach to binding mode and affinity estimation of estrogens
(2013)
Fuzzy spectral clustering by PCCA+: application to Markov state models and data classification
(2013)
Obtaining a sufficient sampling of conformational space is a common problem in molecular simulation. We present the implementation of an umbrella-like adaptive sampling approach based on function-based meshless discretization of conformational space that is compatible with state of the art molecular dynamics code and that integrates an eigenvector-based clustering approach for conformational analysis and the computation of inter-conformational transition rates. The approach is applied to three example systems, namely n-pentane, alanine dipeptide, and a small synthetic host-guest system, the latter two including explicitly modeled solvent.