TY - JOUR
T1 - Resolution exchange simulation
AU - Lyman, Edward
AU - Ytreberg, F. Marty
AU - Zuckerman, Daniel M.
PY - 2006/1/20
Y1 - 2006/1/20
N2 - We extend replica-exchange simulation in two ways and apply our approaches to biomolecules. The first generalization permits exchange simulation between models of differing resolution-i.e., between detailed and coarse-grained models. Such "resolution exchange" can be applied to molecular systems or spin systems. The second extension is to "pseudoexchange" simulations, which require little CPU usage for most levels of the exchange ladder and also substantially reduce the need for overlap between levels. Pseudoexchanges can be used in either replica or resolution exchange simulations. We perform efficient, converged simulations of a 50-atom peptide to illustrate the new approaches.
AB - We extend replica-exchange simulation in two ways and apply our approaches to biomolecules. The first generalization permits exchange simulation between models of differing resolution-i.e., between detailed and coarse-grained models. Such "resolution exchange" can be applied to molecular systems or spin systems. The second extension is to "pseudoexchange" simulations, which require little CPU usage for most levels of the exchange ladder and also substantially reduce the need for overlap between levels. Pseudoexchanges can be used in either replica or resolution exchange simulations. We perform efficient, converged simulations of a 50-atom peptide to illustrate the new approaches.
UR - http://www.scopus.com/inward/record.url?scp=32644458379&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=32644458379&partnerID=8YFLogxK
U2 - 10.1103/PhysRevLett.96.028105
DO - 10.1103/PhysRevLett.96.028105
M3 - Article
C2 - 16486650
AN - SCOPUS:32644458379
SN - 0031-9007
VL - 96
JO - Physical Review Letters
JF - Physical Review Letters
IS - 2
M1 - 028105
ER -