ZIBgridfree: efficient conformational analysis by partition-of-unity coupling.

Bujotzek, Alexander; Schütt, Ole; Nielsen, Adam; Fackeldey, Konstantin; Weber, Marcus

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.

CONFORMATIONAL analysis; PENTANE; COUPLING reactions (Chemistry); ALANINE; DISCRETIZATION methods; MOLECULAR dynamics; SIMULATION methods & models

Journal of Mathematical Chemistry, 2014, Vol 52, Issue 3, p781

0259-9791

Academic Journal

10.1007/s10910-013-0265-1