Abstract
Milestoning is a method aimed at reconstructing the statistical properties of the long-time dynamics of a system by exploiting the crossing statistics of a set of hypersurfaces, called the "milestones", placed along the reaction coordinate [Faradjian and Elber, J. Chem. Phys. 2004, 120, 10880]. Recently, Vanden-Eijnden and Venturoli [J. Chem. Phys. 2009, 130, 194101] showed that when a complete Voronoi tessellation of the configurational space is available, milestoning can be reformulated to utilize the statistics from a series of independent simulations, each confined within a single cell via strict reflections at the boundaries. As a byproduct, this "Voronoi tessellated milestoning" method also permits to compute the free energy of the tessellation. Here, the method is extended to support the usage of differentiable restraining potentials to confine the trajectories within each cell.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 2589-2594 |
| Number of pages | 6 |
| Journal | Journal of Chemical Theory and Computation |
| Volume | 5 |
| Issue number | 10 |
| DOIs | |
| State | Published - Oct 2009 |
Fingerprint
ASJC Scopus subject areas
- Physical and Theoretical Chemistry
- Computer Science Applications
Cite this
Free energy and kinetics of conformational transitions from voronoi tessellated milestoning with restraining potentials. / Maragliano, Luca; Vanden Eijnden, Eric; Roux, Benoît.
In: Journal of Chemical Theory and Computation, Vol. 5, No. 10, 10.2009, p. 2589-2594.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Free energy and kinetics of conformational transitions from voronoi tessellated milestoning with restraining potentials
AU - Maragliano, Luca
AU - Vanden Eijnden, Eric
AU - Roux, Benoît
PY - 2009/10
Y1 - 2009/10
N2 - Milestoning is a method aimed at reconstructing the statistical properties of the long-time dynamics of a system by exploiting the crossing statistics of a set of hypersurfaces, called the "milestones", placed along the reaction coordinate [Faradjian and Elber, J. Chem. Phys. 2004, 120, 10880]. Recently, Vanden-Eijnden and Venturoli [J. Chem. Phys. 2009, 130, 194101] showed that when a complete Voronoi tessellation of the configurational space is available, milestoning can be reformulated to utilize the statistics from a series of independent simulations, each confined within a single cell via strict reflections at the boundaries. As a byproduct, this "Voronoi tessellated milestoning" method also permits to compute the free energy of the tessellation. Here, the method is extended to support the usage of differentiable restraining potentials to confine the trajectories within each cell.
AB - Milestoning is a method aimed at reconstructing the statistical properties of the long-time dynamics of a system by exploiting the crossing statistics of a set of hypersurfaces, called the "milestones", placed along the reaction coordinate [Faradjian and Elber, J. Chem. Phys. 2004, 120, 10880]. Recently, Vanden-Eijnden and Venturoli [J. Chem. Phys. 2009, 130, 194101] showed that when a complete Voronoi tessellation of the configurational space is available, milestoning can be reformulated to utilize the statistics from a series of independent simulations, each confined within a single cell via strict reflections at the boundaries. As a byproduct, this "Voronoi tessellated milestoning" method also permits to compute the free energy of the tessellation. Here, the method is extended to support the usage of differentiable restraining potentials to confine the trajectories within each cell.
UR - http://www.scopus.com/inward/record.url?scp=73949127824&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=73949127824&partnerID=8YFLogxK
U2 - 10.1021/ct900279z
DO - 10.1021/ct900279z
M3 - Article
AN - SCOPUS:73949127824
VL - 5
SP - 2589
EP - 2594
JO - Journal of Chemical Theory and Computation
JF - Journal of Chemical Theory and Computation
SN - 1549-9618
IS - 10
ER -