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%% Created for Dan Gezelter at 2010-10-18 13:05:47 -0400 |
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@string{prl = {Phys. Rev. Lett.}} |
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@string{rmp = {Rev. Mod. Phys.}} |
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@article{ISI:A1984TQ73500045, |
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Author = {BERENDSEN, HJC and POSTMA, JPM and VANGUNSTEREN, WF and DINOLA, A and HAAK, JR}, |
| 62 |
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Date-Added = {2010-10-18 13:04:11 -0400}, |
| 63 |
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Date-Modified = {2010-10-18 13:04:11 -0400}, |
| 64 |
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Journal = {JOURNAL OF CHEMICAL PHYSICS}, |
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Journal-Iso = {J. Chem. Phys.}, |
| 66 |
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Number = {8}, |
| 67 |
+ |
Pages = {3684-3690}, |
| 68 |
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Title = {MOLECULAR-DYNAMICS WITH COUPLING TO AN EXTERNAL BATH}, |
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Volume = {81}, |
| 70 |
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Year = {1984} |
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} |
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@article{ANDERSEN:1980vn, |
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Address = {WOODBURY}, |
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Author = {ANDERSEN, H. C.}, |
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Cited-Reference-Count = {29}, |
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Date-Added = {2010-10-18 13:01:27 -0400}, |
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Date-Modified = {2010-10-18 13:01:27 -0400}, |
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Document-Type = {Article}, |
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Isi = {ISI:A1980JK06800026}, |
| 81 |
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Isi-Document-Delivery-Number = {JK068}, |
| 82 |
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Iso-Source-Abbreviation = {J. Chem. Phys.}, |
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Issn = {0021-9606}, |
| 84 |
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Journal = {JOURNAL OF CHEMICAL PHYSICS}, |
| 85 |
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Language = {English}, |
| 86 |
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Number = {4}, |
| 87 |
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Page-Count = {10}, |
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Pages = {2384--2393}, |
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Publication-Type = {J}, |
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Publisher = {AMER INST PHYSICS}, |
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Publisher-Address = {CIRCULATION FULFILLMENT DIV, 500 SUNNYSIDE BLVD, WOODBURY, NY 11797-2999}, |
| 92 |
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Reprint-Address = {ANDERSEN, HC, STANFORD UNIV,DEPT CHEM,STANFORD,CA 94305.}, |
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Source = {J CHEM PHYS}, |
| 94 |
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Subject-Category = {Physics, Atomic, Molecular & Chemical}, |
| 95 |
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Times-Cited = {2017}, |
| 96 |
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Title = {MOLECULAR-DYNAMICS SIMULATIONS AT CONSTANT PRESSURE AND-OR TEMPERATURE}, |
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Volume = {72}, |
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Year = {1980}} |
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|
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@article{Sturgeon:2000kx, |
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Abstract = {We present a new algorithm for isothermal-isobaric molecular-dynamics simulation. The method uses an extended Hamiltonian with an Andersen piston combined with the Nose-Poincare thermostat, recently developed by Bond, Leimkuhler, and Laird [J. Comp. Phys. 151, 114 (1999)]. This Nose-Poincare-Andersen (NPA) formulation has advantages over the Nose-Hoover-Andersen approach in that the NPA is Hamiltonian and can take advantage of symplectic integration schemes, which lead to enhanced stability for long-time simulations. The equations of motion are integrated using a generalized leapfrog algorithm (GLA) and the method is easy to implement, symplectic, explicit, and time reversible. To demonstrate the superior stability of the method we show results for test simulations using a model for aluminum and compare it to a recently developed time-reversible algorithm for Nose-Hoover-Anderson. In addition, an extension of the NPA to multiple time steps is outlined and a symplectic and time-reversible integration algorithm, based on the GLA, is given. (C) 2000 American Institute of Physics. [S0021-9606(00)51307-5].}, |
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Address = {2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA}, |
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Author = {Sturgeon, JB and Laird, BB}, |
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Date-Added = {2010-10-18 13:00:24 -0400}, |
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Date-Modified = {2010-10-18 13:00:24 -0400}, |
| 106 |
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Isi = {000085345300002}, |
| 107 |
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Isi-Recid = {113793583}, |
| 108 |
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Isi-Ref-Recids = {81972786 39595345 109970205 51854999 66009108 53306123 99223832 60134148 54857943 67654925 80228604 52514734 52893114 79704395 68016955 83328866 101670717 73702456 44796632 88334077 95381668 80404775}, |
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Journal = {Journal of Chemical Physics}, |
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Month = feb, |
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Number = {8}, |
| 112 |
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Pages = {3474--3482}, |
| 113 |
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Publisher = {AMER INST PHYSICS}, |
| 114 |
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Times-Cited = {46}, |
| 115 |
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Title = {Symplectic algorithm for constant-pressure molecular dynamics using a Nose-Poincare thermostat}, |
| 116 |
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Volume = {112}, |
| 117 |
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Year = {2000}, |
| 118 |
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Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000085345300002}} |
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@article{FELLER:1995fk, |
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Abstract = {A new method for performing molecular dynamics simulations under constant pressure is presented. In the method, which is based on the extended system formalism introduced by Andersen, the deterministic equations of motion for the piston degree of freedom are replaced by a Langevin equation; a suitable choice of collision frequency then eliminates the unphysical ''ringing'' of the volume associated with the piston mass. In this way it is similar to the ''weak coupling algorithm'' developed by Berendsen and co-workers to perform molecular dynamics simulation without piston mass effects. It is shown, however, that the weak coupling algorithm induces artifacts into the simulation which can be quite severe for inhomogeneous systems such as aqueous biopolymers or liquid/liquid interfaces.}, |
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Address = {CIRCULATION FULFILLMENT DIV, 500 SUNNYSIDE BLVD, WOODBURY, NY 11797-2999}, |
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Author = {FELLER, SE and ZHANG, YH and PASTOR, RW and BROOKS, BR}, |
| 124 |
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Date-Added = {2010-10-18 12:59:12 -0400}, |
| 125 |
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Date-Modified = {2010-10-18 12:59:12 -0400}, |
| 126 |
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Isi = {A1995RU11000023}, |
| 127 |
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Isi-Recid = {92912418}, |
| 128 |
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Isi-Ref-Recids = {64516210 39595345 53816621 49016001 49016003 92912419 52031423 49377405 61751037 8052804 92912420 88334077 51117777 53442503 92912421 13886649 31384453 87659780 85624658 53101078 87752055 92912422}, |
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Journal = {Journal of Chemical Physics}, |
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Month = sep, |
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Number = {11}, |
| 132 |
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Pages = {4613--4621}, |
| 133 |
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Publisher = {AMER INST PHYSICS}, |
| 134 |
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Times-Cited = {603}, |
| 135 |
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Title = {CONSTANT-PRESSURE MOLECULAR-DYNAMICS SIMULATION - THE LANGEVIN PISTON METHOD}, |
| 136 |
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Volume = {103}, |
| 137 |
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Year = {1995}, |
| 138 |
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Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=A1995RU11000023}} |
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@article{Jakobsen:2005uq, |
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Abstract = {We present a method for constant-pressure and constant-surface tension simulations in dissipative particle dynamics using a Langevin piston approach. We demonstrate that the corresponding equations of motion lead to the relevant ensembles and propose an appropriate scheme of integration. After having identified a suitable set of parameters for the approach, we demonstrate the feasibility of the approach by applying it to two different systems, a simple isotropic fluid and an anisotropic fluid lipid-bilayer membrane in water. Results are presented for, respectively, isothermal bulk compressibility, tracer diffusion coefficient, lipid head-group area, and isothermal area compressibility. We find that our Langevin piston approach leads to improvements over other approaches in terms of faster equilibration and shorter correlation times of various system variables.}, |
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Address = {CIRCULATION \& FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA}, |
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Author = {Jakobsen, AF}, |
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Date-Added = {2010-10-18 12:59:12 -0400}, |
| 145 |
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Date-Modified = {2010-10-18 12:59:12 -0400}, |
| 146 |
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Doi = {DOI 10.1063/1.1867374}, |
| 147 |
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Isi = {000228287900056}, |
| 148 |
+ |
Isi-Recid = {143814862}, |
| 149 |
+ |
Isi-Ref-Recids = {72962882 39595345 143814863 91397367 92912418 110813457 111518806 49778585 102083652 120914607 80001319 54857943 111485260 88334077 95381668 130520135 41081337 135065719 126224491 120652643 108464729 123676541 127189050 123938968}, |
| 150 |
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Journal = {Journal of Chemical Physics}, |
| 151 |
+ |
Month = mar, |
| 152 |
+ |
Number = {12}, |
| 153 |
+ |
Publisher = {AMER INST PHYSICS}, |
| 154 |
+ |
Times-Cited = {44}, |
| 155 |
+ |
Title = {Constant-pressure and constant-surface tension simulations in dissipative particle dynamics}, |
| 156 |
+ |
Volume = {122}, |
| 157 |
+ |
Year = {2005}, |
| 158 |
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Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000228287900056}} |
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@misc{openmd, |
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Author = {J. Daniel Gezelter and Shenyu Kuang and James Marr and Kelsey Stocker and Chunlei Li and Charles F. Vardeman and Teng Lin and Christopher J. Fennell and Xiuquan Sun and Kyle Daily and Yang Zheng and Matthew A. Meineke}, |
