PAZÚRIKOVÁ, Jana, Aleš KŘENEK, Vojtěch SPIWOK a Mária ŠIMKOVÁ. Reducing the number of mean-square deviation calculations with floating close structure in metadynamics. Journal of Chemical Physics. Melville: American Institute of Physics, 2017, roč. 146, č. 11, s. "115101:1"-"115101:8", 8 s. ISSN 0021-9606. Dostupné z: https://dx.doi.org/10.1063/1.4978296. |
Další formáty:
BibTeX
LaTeX
RIS
@article{1386007, author = {Pazúriková, Jana and Křenek, Aleš and Spiwok, Vojtěch and Šimková, Mária}, article_location = {Melville}, article_number = {11}, doi = {http://dx.doi.org/10.1063/1.4978296}, keywords = {Conformational dynamics; Free energy; Eigenvalues; Low dimensional topology; Biomolecular conformation;Approximation}, language = {eng}, issn = {0021-9606}, journal = {Journal of Chemical Physics}, title = {Reducing the number of mean-square deviation calculations with floating close structure in metadynamics}, url = {http://aip.scitation.org/doi/abs/10.1063/1.4978296}, volume = {146}, year = {2017} }
TY - JOUR ID - 1386007 AU - Pazúriková, Jana - Křenek, Aleš - Spiwok, Vojtěch - Šimková, Mária PY - 2017 TI - Reducing the number of mean-square deviation calculations with floating close structure in metadynamics JF - Journal of Chemical Physics VL - 146 IS - 11 SP - "115101:1"-"115101:8" EP - "115101:1"-"115101:8" PB - American Institute of Physics SN - 00219606 KW - Conformational dynamics KW - Free energy KW - Eigenvalues KW - Low dimensional topology KW - Biomolecular conformation;Approximation UR - http://aip.scitation.org/doi/abs/10.1063/1.4978296 L2 - http://aip.scitation.org/doi/abs/10.1063/1.4978296 N2 - 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. Published by AIP Publishing. ER -
PAZÚRIKOVÁ, Jana, Aleš KŘENEK, Vojtěch SPIWOK a Mária ŠIMKOVÁ. Reducing the number of mean-square deviation calculations with floating close structure in metadynamics. \textit{Journal of Chemical Physics}. Melville: American Institute of Physics, 2017, roč.~146, č.~11, s.~''115101:1''-''115101:8'', 8 s. ISSN~0021-9606. Dostupné z: https://dx.doi.org/10.1063/1.4978296.
|