title: Molecular dynamics in principal component space.
abstract: A molecular dynamics algorithm in principal component space is presented. It is demonstrated that sampling can be improved without changing the ensemble by assigning masses to the principal components proportional to the inverse square root of the eigenvalues. The setup of the simulation requires no prior knowledge of the system; a short initial MD simulation to extract the eigenvectors and eigenvalues suffices. Independent measures indicated a 6-7 times faster sampling compared to a regular molecular dynamics simulation.
authors.affiliation: Department of Chemistry, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium. servaas.michielssens@chem.kuleuven.be
authors.forename: Servaas
authors.initials: S
authors.lastname: Michielssens
authors.forename: Titus S
authors.initials: TS
authors.lastname: van Erp
authors.forename: Carsten
authors.initials: C
authors.lastname: Kutzner
authors.forename: Arnout
authors.initials: A
authors.lastname: Ceulemans
authors.forename: Bert L
authors.initials: BL
authors.lastname: de Groot
mesh_terms: D000465:Algorithms; D056004:Molecular Dynamics Simulation / Q000191:economics; D008970:Molecular Weight; D025341:Principal Component Analysis; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry; D013816:Thermodynamics; D013997:Time Factors
chemical_list: D011506:Proteins