Reducing the number of mean-square deviation calculations with floating close structure in metadynamics.
Metadynamics is an important collective-coordinate-based enhanced sampling simulation method. Its performance depends significantly on the capability of collective coordinates to describe the studied molecular processes. Collective coordinates based on comparison with reference landmark structures can be used to enhance sampling in highly complex systems; however, they may slow down simulations due to high number of structure-structure distance (e.g., mean-square deviation) calculations. Here we introduce an approximation of root-mean-square or mean-square deviation that significantly reduces numbers of computationally expensive operations. We evaluate its accuracy and theoretical performance gain with metadynamics simulations on two molecular systems.
Institute of Computer Science, Masaryk University, Brno, Czech Republic.
Jana
0000000161247080
J
Pazúriková
Institute of Computer Science, Masaryk University, Brno, Czech Republic.
Aleš
0000000233953196
A
Křenek
Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czech Republic.
Vojtěch
V
Spiwok
Institute of Computer Science, Masaryk University, Brno, Czech Republic.
Mária
M
Šimková