Greedy replica exchange algorithm for heterogeneous computing grids
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| 024 | 7 | 0 | |a 10.1007/s00894-015-2763-5 |2 doi |
| 035 | |a (NATIONALLICENCE)springer-10.1007/s00894-015-2763-5 | ||
| 245 | 0 | 0 | |a Greedy replica exchange algorithm for heterogeneous computing grids |h [Elektronische Daten] |c [Christopher Lockhart, James O'Connor, Steven Armentrout, Dmitri Klimov] |
| 520 | 3 | |a Replica exchange molecular dynamics (REMD) has become a valuable tool in studying complex biomolecular systems. However, its application on distributed computing grids is limited by the heterogeneity of this environment. In this study, we propose a REMD implementation referred to as greedy REMD (gREMD) suitable for computations on heterogeneous grids. To decentralize replica management, gREMD utilizes a precomputed schedule of exchange attempts between temperatures. Our comparison of gREMD against standard REMD suggests four main conclusions. First, gREMD accelerates grid REMD simulations by as much as 40 %. Second, gREMD increases CPU utilization rates in grid REMD by up to 60 %. Third, we argue that gREMD is expected to maintain approximately constant CPU utilization rates and simulation wall-clock times with the increase in the number of replicas. Finally, we show that gREMD correctly implements the REMD algorithm and reproduces the conformational ensemble of a short peptide sampled in our previous standard REMD simulations. We believe that gREMD can find its place in large-scale REMD simulations on heterogeneous computing grids. Graphical Abstract Standard replica exchange molecular dynamics (REMD) typically requires all replicas to complete prior to initiation of the replica exchange protocol. Greedy REMD decentralizes this process and therefore only requires a replica and its predetermined exchange partner to have finished simulations prior to initiating replica exchange. Because greedy REMD reduces the idle time associated with replica exchange tasks, it becomes particularly well suited for performing REMD on heterogeneous distributed computing environments. | |
| 540 | |a Springer-Verlag Berlin Heidelberg, 2015 | ||
| 690 | 7 | |a Replica exchange molecular dynamics |2 nationallicence | |
| 690 | 7 | |a Conformational sampling |2 nationallicence | |
| 690 | 7 | |a Distributed grid-based simulations |2 nationallicence | |
| 690 | 7 | |a Decentralized replica management |2 nationallicence | |
| 690 | 7 | |a A β peptide |2 nationallicence | |
| 700 | 1 | |a Lockhart |D Christopher |u School of Systems Biology, George Mason University, 20110, Manassas, VA, USA |4 aut | |
| 700 | 1 | |a O'Connor |D James |u Parabon Computation Inc., 11260 Roger Bacon Drive, Suite 406, 20190, Reston, VA, USA |4 aut | |
| 700 | 1 | |a Armentrout |D Steven |u Parabon Computation Inc., 11260 Roger Bacon Drive, Suite 406, 20190, Reston, VA, USA |4 aut | |
| 700 | 1 | |a Klimov |D Dmitri |u School of Systems Biology, George Mason University, 20110, Manassas, VA, USA |4 aut | |
| 773 | 0 | |t Journal of Molecular Modeling |d Springer Berlin Heidelberg |g 21/9(2015-09-01), 1-12 |x 1610-2940 |q 21:9<1 |1 2015 |2 21 |o 894 | |
| 856 | 4 | 0 | |u https://doi.org/10.1007/s00894-015-2763-5 |q text/html |z Onlinezugriff via DOI |
| 898 | |a BK010053 |b XK010053 |c XK010000 | ||
| 900 | 7 | |a Metadata rights reserved |b Springer special CC-BY-NC licence |2 nationallicence | |
| 908 | |D 1 |a research-article |2 jats | ||
| 949 | |B NATIONALLICENCE |F NATIONALLICENCE |b NL-springer | ||
| 950 | |B NATIONALLICENCE |P 856 |E 40 |u https://doi.org/10.1007/s00894-015-2763-5 |q text/html |z Onlinezugriff via DOI | ||
| 950 | |B NATIONALLICENCE |P 700 |E 1- |a Lockhart |D Christopher |u School of Systems Biology, George Mason University, 20110, Manassas, VA, USA |4 aut | ||
| 950 | |B NATIONALLICENCE |P 700 |E 1- |a O'Connor |D James |u Parabon Computation Inc., 11260 Roger Bacon Drive, Suite 406, 20190, Reston, VA, USA |4 aut | ||
| 950 | |B NATIONALLICENCE |P 700 |E 1- |a Armentrout |D Steven |u Parabon Computation Inc., 11260 Roger Bacon Drive, Suite 406, 20190, Reston, VA, USA |4 aut | ||
| 950 | |B NATIONALLICENCE |P 700 |E 1- |a Klimov |D Dmitri |u School of Systems Biology, George Mason University, 20110, Manassas, VA, USA |4 aut | ||
| 950 | |B NATIONALLICENCE |P 773 |E 0- |t Journal of Molecular Modeling |d Springer Berlin Heidelberg |g 21/9(2015-09-01), 1-12 |x 1610-2940 |q 21:9<1 |1 2015 |2 21 |o 894 | ||