Promoting transparency and reproducibility in enhanced molecular simulations

被引：707

作者：

Bonomi, Massimiliano ^{[1
,2
]}

Bussi, Giovanni ^{[3
]}

Camilloni, Carlo ^{[4
]}

Tribello, Gareth A. ^{[5
]}

Banas, Pavel ^{[6
]}

Barducci, Alessandro ^{[7
,8
,9
,10
]}

Bernetti, Mattia ^{[3
]}

Bolhuis, Peter G. ^{[11
]}

Bottaro, Sandro ^{[12
]}

Branduardi, Davide ^{[13
]}

Capelli, Riccardo ^{[14
]}

Carloni, Paolo ^{[14
]}

Ceriotti, Michele ^{[15
,16
]}

Cesari, Andrea ^{[3
]}

Chen, Haochuan ^{[17
]}

Chen, Wei ^{[18
]}

Colizzi, Francesco ^{[19
]}

De, Sandip ^{[20
,77
]}

De La Pierre, Marco ^{[21
]}

Donadio, Davide ^{[22
]}

Drobot, Viktor ^{[23
]}

Ensing, Bernd ^{[11
]}

Ferguson, Andrew L. ^{[24
]}

Filizola, Marta ^{[25
]}

Fraser, James S. ^{[26
,27
]}

Fu, Haohao ^{[17
]}

Gasparotto, Piero ^{[28
,29
]}

Gervasio, Francesco Luigi ^{[30
,31
]}

Giberti, Federico ^{[15
,16
]}

Gil-Ley, Alejandro ^{[32
]}

Giorgino, Toni ^{[33
]}

Heller, Gabriella T. ^{[34
]}

Hocky, Glen M. ^{[35
]}

Iannuzzi, Marcella ^{[36
]}

Invernizzi, Michele ^{[37
,38
]}

Jelfs, Kim E. ^{[39
]}

Jussupow, Alexander ^{[40
,41
]}

Kirilin, Evgeny ^{[42
]}

Laio, Alessandro ^{[3
,43
]}

Limongelli, Vittorio ^{[44
,45
]}

Lindorff-Larsen, Kresten ^{[46
]}

Lohr, Thomas ^{[34
]}

Marinelli, Fabrizio ^{[32
]}

Martin-Samos, Layla ^{[47
]}

Masetti, Matteo ^{[48
]}

Meyer, Ralf ^{[49
]}

Michaelides, Angelos ^{[28
,29
,48
]}

Molteni, Carla ^{[50
]}

Morishita, Tetsuya ^{[51
]}

Nava, Marco ^{[52
]}

机构：

[1] Inst Pasteur, Dept Struct Biol & Chem, Paris, France

[2] CNRS, UMR 3528, Paris, France

[3] Int Sch Adv Studies SISSA, Trieste, Italy

[4] Univ Milan, Dipartimento Biosci, Milan, Italy

[5] Queens Univ Belfast, Atomist Simulat Ctr, Belfast, Antrim, North Ireland

[6] Palacky Univ, Fac Sci, Olomouc, Czech Republic

[7] Ctr Biochim Struct Montpellier, Montpellier, France

[8] CNRS, UMR 5048, Montpellier, France

[9] INSERM, U 1054, Montpellier, France

[10] Univ Montpellier, Montpellier, France

[11] Univ Amsterdam, Vant Hoff Inst Mol Sci, Amsterdam, Netherlands

[12] Italian Inst Technol, Genoa, Italy

[13] Schrodinger Inc, Cambridge, England

[14] Forschungszentrum Julich, Computat Biomed IAS 5 INM 9, Julich, Germany

[15] Ecole Polytech Federale Lausanne, Inst Mat, Lausanne, Switzerland

[16] Natl Ctr Computat Design & Discovery Novel Mat MA, Lausanne, Switzerland

[17] Nankai Univ, Coll Chem, Res Ctr Analyt Sci, Tianjin, Peoples R China

[18] Univ Illinois, Dept Phys, Urbana, IL USA

[19] BIST, Inst Res Biomed IRB Barcelona, Barcelona, Spain

[20] Ecole Polytech Federale Lausanne, Inst Mat, Lausanne, Switzerland

[21] Pawsey Supercomp Ctr, Kensington, NSW, Australia

[22] Univ Calif Davis, Dept Chem, Davis, CA 95616 USA

[23] Lomonosov Moscow State Univ, Dept Chem, Moscow, Russia

[24] Univ Chicago, Pritzker Sch Mol Engn, Chicago, IL 60637 USA

[25] Icahn Sch Med Mt Sinai, Dept Pharmacol Sci, New York, NY 10029 USA

[26] Univ Calif San Francisco, Dept Bioengn & Therapeut Sci, San Francisco, CA 94143 USA

[27] Univ Calif San Francisco, Calif Inst Quantitat Biol, San Francisco, CA 94143 USA

[28] UCL, Dept Phys & Astron, London, England

[29] Thomas Young Ctr, London, England

[30] UCL, Dept Chem, London, England

[31] UCL, Inst Struct & Mol Biol, London, England

[32] NHLBI, NIH, Bldg 10, Bethesda, MD 20892 USA

[33] CNR, Biophys Inst, IBF CNR, Milan, Italy

[34] Univ Cambridge, Dept Chem, Cambridge, England

[35] NYU, Dept Chem, New York, NY USA

[36] Univ Zurich, Dept Chem, Zurich, Switzerland

[37] Swiss Fed Inst Technol, Dept Phys, Lugano, Switzerland

[38] Univ Svizzera Italiana, Fac Informat, Lugano, Switzerland

[39] Imperial Coll London, Dept Chem, London, England

[40] Tech Univ Munich, Dept Chem, Garching, Germany

[41] Tech Univ Munich, Inst Adv Study, Garching, Germany

[42] Lomonosov Moscow State Univ, Belozersky Inst Phys Chem Biol, Moscow, Russia

[43] Abdus Salaam Int Ctr Theoret Phys, Trieste, Italy

[44] Univ Svizzera Italiana, Inst Computat Sci, Fac Biomed Sci, Lugano, Switzerland

[45] Univ Naples Federico II, Dept Pharm, Naples, Italy

[46] Univ Copenhagen, Dept Biol, Copenhagen, Denmark

[47] Ist Off Mat, CNR IOM Democritos Natl Simulat Ctr, Trieste, Italy

[48] Univ Bologna, Alma Mater Studiorum, Dept Pharm & Biotechnol, Bologna, Italy

[49] Graz Univ Technol, Inst Expt Phys, Graz, Austria

[50] Kings Coll London, Dept Phys, London, England

来源：

NATURE METHODS | 2019年 / 16卷 / 08期

基金：

英国工程与自然科学研究理事会;

关键词：

DYNAMICS;

D O I：

10.1038/s41592-019-0506-8

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

The PLUMED consortium unifies developers and contributors to PLUMED, an open-source library for enhanced-sampling, free-energy calculations and the analysis of molecular dynamics simulations. Here, we outline our efforts to promote transparency and reproducibility by disseminating protocols for enhanced-sampling molecular simulations.

引用

页码：670 / 673

页数：4