4257
eng
reportzib
0
2013-09-27
2013-09-27
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Efficient Conformational Analysis by Partition-of-Unity Coupling
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.
Math Chem
1438-0064
urn:nbn:de:0297-zib-42570
Alexander Bujotzek
Konstantin Fackeldey
Ole Schütt
Adam Nielsen
Konstantin Fackeldey
Marcus Weber
ZIB-Report
13-58
eng
uncontrolled
Markov State Models
eng
uncontrolled
Meshfree
eng
uncontrolled
Molecular Simulation
eng
uncontrolled
Partition of Unity
MATHEMATICAL SOFTWARE
Markov processes (NEW)
General theory and mathematical aspects
Markov processes
Computational methods
Numerical Mathematics
Computational Molecular Design
Fackeldey, Konstantin
Weber, Marcus
BMS-Nielsen
Matheon-A19
MIP_FORMATION
NAMPAR
Salsa-Klimm
SFB1114-A5
SFB765-C2
https://opus4.kobv.de/opus4-zib/files/4257/MolPyPUM.pdf
4658
2014
deu
781
804
3
52
article
0
--
--
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ZIBgridfree: Efficient Conformational Analysis by Partition-of-Unity Coupling
Journal of Mathematical Chemistry
10.1007/s10910-013-0265-1
yes
urn:nbn:de:0297-zib-42570
Alexander Bujotzek
Adam Nielsen
Ole Schütt
Adam Nielsen
Konstantin Fackeldey
Marcus Weber
Numerical Mathematics
Computational Molecular Design
Fackeldey, Konstantin
Weber, Marcus
BMS-Nielsen
Matheon-A19
MIP_FORMATION
NAMPAR
Salsa-Klimm
SFB1114-A5
SFB765-C2