EPJ Special Topics (EPJ ST)

Open Access

Editorial

Scale bridging in molecular simulation - Recurrent problems and current options p. 2173

Carsten Hartmann and Luigi Delle Site

Published online: 21 September 2015

DOI: 10.1140/epjst/e2015-02406-y

Review

Thermodynamic consistency and other challenges in coarse-graining models p. 2177

M. Guenza

Published online: 22 June 2015

DOI: 10.1140/epjst/e2015-02407-x

Review

A generalized-Yvon-Born-Green method for coarse-grained modeling - Advances, Challenges, and Insight p. 2193

J.F. Rudzinski and W.G. Noid

Published online: 22 June 2015

DOI: 10.1140/epjst/e2015-02408-9

Multiscale molecular dynamics/hydrodynamics implementation of two dimensional “Mercedes Benz” water model p. 2217

A. Scukins, D. Nerukh, E. Pavlov, S. Karabasov and A. Markesteijn

Published online: 22 June 2015

DOI: 10.1140/epjst/e2015-02409-8

Coarse-graining polymer solutions: A critical appraisal of single- and multi-site models p. 2239

G. D'Adamo, R. Menichetti, A. Pelissetto and C. Pierleoni

Published online: 22 June 2015

DOI: 10.1140/epjst/e2015-02410-3

Adaptive resolution simulation in equilibrium and beyond p. 2269

H. Wang and A. Agarwal

Published online: 22 June 2015

DOI: 10.1140/epjst/e2015-02411-2

Advantages and challenges in coupling an ideal gas to atomistic models in adaptive resolution simulations p. 2289

K. Kreis, A.C. Fogarty, K. Kremer and R. Potestio

Published online: 22 June 2015

DOI: 10.1140/epjst/e2015-02412-1

Review

An introduction to the problem of bridging quantum and classical dynamics p. 2305

S. Bonella and G. Ciccotti

Published online: 22 June 2015

DOI: 10.1140/epjst/e2015-02413-0

Continuum simulations of water flow past fullerene molecules p. 2321

A. Popadić, M. Praprotnik, P. Koumoutsakos and J.H. Walther

Published online: 22 June 2015

DOI: 10.1140/epjst/e2015-02414-y

Review

Open boundary molecular dynamics p. 2331

R. Delgado-Buscalioni, J. Sablić and M. Praprotnik

Published online: 22 June 2015

DOI: 10.1140/epjst/e2015-02415-x

Effective interactions and large deviations in stochastic processes p. 2351

R.L. Jack and P. Sollich

Published online: 22 June 2015

DOI: 10.1140/epjst/e2015-02416-9

Reactive flows and unproductive cycles for random walks on complex networks p. 2369

R. Banisch, N. Djurdjevac Conrad and Ch. Schütte

Published online: 22 June 2015

DOI: 10.1140/epjst/e2015-02417-8

Review

Free energies for rare events: Temperature accelerated MD and MC p. 2389

S. Meloni and G. Ciccotti

Published online: 22 June 2015

DOI: 10.1140/epjst/e2015-02418-7

Review

Practical and conceptual path sampling issues p. 2409

P.G. Bolhuis and C. Dellago

Published online: 22 June 2015

DOI: 10.1140/epjst/e2015-02419-6

Review

Accelerated dynamics: Mathematical foundations and algorithmic improvements p. 2429

T. Lelièvre

Published online: 22 June 2015

DOI: 10.1140/epjst/e2015-02420-1

Review

A critical appraisal of Markov state models p. 2445

Ch. Schütte and M. Sarich

Published online: 22 June 2015

DOI: 10.1140/epjst/e2015-02421-0

Pseudo generators for under-resolved molecular dynamics p. 2463

A. Bittracher, C. Hartmann, O. Junge and P. Koltai

Published online: 22 June 2015

DOI: 10.1140/epjst/e2015-02422-y

Advancements in multi scale modeling: Adaptive resolution simulations and related issues p. 2491

Marina G. Guenza

Published online: 21 September 2015

DOI: 10.1140/epjst/e2015-02529-1

Comments on “Adaptive resolution simulation in equilibrium and beyond” by H. Wang and A. Agarwal p. 2497

R. Klein

Published online: 21 September 2015

DOI: 10.1140/epjst/e2015-02530-8

Reply to comment by R. Klein on “Adaptive resolution simulation in equilibrium and beyond” p. 2501

Han Wang and Animesh Agarwal

Published online: 21 September 2015

DOI: 10.1140/epjst/e2015-02531-7

Comments on “Advantages and challenges in coupling an ideal gas to atomistic models in adaptive resolution simulations” by K. Kreis, A.C. Fogarty, K. Kremer and R. Potestio p. 2503

R. Klein

Published online: 21 September 2015

DOI: 10.1140/epjst/e2015-02532-6

Reply to comments by R. Klein on Advantages and challenges in coupling an ideal gas to atomistic models in adaptive resolution simulations p. 2505

K. Kreis, A.C. Fogarty, K. Kremer and R. Potestio

Published online: 21 September 2015

DOI: 10.1140/epjst/e2015-02533-5

Comment on “An introduction to the problem of bridging quantum and classical dynamics” by S. Bonella and G. Ciccotti p. 2507

B. Leimkuhler

Published online: 21 September 2015

DOI: 10.1140/epjst/e2015-02534-4

Comments on “Open boundary molecular dynamics” by R. Delgado-Buscalioni, J. Sablić and M. Praprotnik p. 2509

R. Klein

Published online: 21 September 2015

DOI: 10.1140/epjst/e2015-02535-3

Reply to comments by R. Klein on “Open boundary molecular dynamics” p. 2511

R. Delgado-Buscalioni, J. Sablić and M. Praprotnik

Published online: 21 September 2015

DOI: 10.1140/epjst/e2015-02536-2

The trees and the forest - Aims and objectives of molecular dynamics simulations p. 2515

G. Ciccotti and E. Vanden-Eijnden

Published online: 21 September 2015

DOI: 10.1140/epjst/e2015-02537-1

Comments on “Reactive flows and unproductive cycles for random walks on complex networks” by R. Banisch, N. Djurdjevac-Conrad and C. Schütte p. 2519

B. Leimkuhler

Published online: 21 September 2015

DOI: 10.1140/epjst/e2015-02538-0

Comments on “A critical appraisal of Markov state models” by M. Sarich and C. Schütte p. 2521

Robert D. Skeel

Published online: 21 September 2015

DOI: 10.1140/epjst/e2015-02539-y

Comment on “Pseudo generators for under-resolved molecular dynamics” by A. Bittracher, C. Hartmann, O. Junge and P. Koltai p. 2525

B. Leimkuhler

Published online: 21 September 2015

DOI: 10.1140/epjst/e2015-02540-6

EPJ

The European Physical Journal Special Topics

Volume 224 / No 12 (2015)

Discussion and Debate: Recurrent Problems in Scale Bridging Techniques in Molecular Simulation – What are the Current Options?

Discussion and Debate: Recurrent Problems in Scale Bridging Techniques in Molecular Simulation – What are the Current Options?

Scale bridging in molecular simulation - Recurrent problems and current options p. 2173

Thermodynamic consistency and other challenges in coarse-graining models p. 2177

A generalized-Yvon-Born-Green method for coarse-grained modeling - Advances, Challenges, and Insight p. 2193

Multiscale molecular dynamics/hydrodynamics implementation of two dimensional “Mercedes Benz” water model p. 2217

Coarse-graining polymer solutions: A critical appraisal of single- and multi-site models p. 2239

Adaptive resolution simulation in equilibrium and beyond p. 2269

Advantages and challenges in coupling an ideal gas to atomistic models in adaptive resolution simulations p. 2289

An introduction to the problem of bridging quantum and classical dynamics p. 2305

Continuum simulations of water flow past fullerene molecules p. 2321

Open boundary molecular dynamics p. 2331

Effective interactions and large deviations in stochastic processes p. 2351

Reactive flows and unproductive cycles for random walks on complex networks p. 2369

Free energies for rare events: Temperature accelerated MD and MC p. 2389

Practical and conceptual path sampling issues p. 2409

Accelerated dynamics: Mathematical foundations and algorithmic improvements p. 2429

A critical appraisal of Markov state models p. 2445

Pseudo generators for under-resolved molecular dynamics p. 2463

Advancements in multi scale modeling: Adaptive resolution simulations and related issues p. 2491

Comments on “Adaptive resolution simulation in equilibrium and beyond” by H. Wang and A. Agarwal p. 2497

Reply to comment by R. Klein on “Adaptive resolution simulation in equilibrium and beyond” p. 2501

Comments on “Advantages and challenges in coupling an ideal gas to atomistic models in adaptive resolution simulations” by K. Kreis, A.C. Fogarty, K. Kremer and R. Potestio p. 2503

Reply to comments by R. Klein on Advantages and challenges in coupling an ideal gas to atomistic models in adaptive resolution simulations p. 2505

Comment on “An introduction to the problem of bridging quantum and classical dynamics” by S. Bonella and G. Ciccotti p. 2507

Comments on “Open boundary molecular dynamics” by R. Delgado-Buscalioni, J. Sablić and M. Praprotnik p. 2509

Reply to comments by R. Klein on “Open boundary molecular dynamics” p. 2511

The trees and the forest - Aims and objectives of molecular dynamics simulations p. 2515

Comments on “Reactive flows and unproductive cycles for random walks on complex networks” by R. Banisch, N. Djurdjevac-Conrad and C. Schütte p. 2519

Comments on “A critical appraisal of Markov state models” by M. Sarich and C. Schütte p. 2521

Comment on “Pseudo generators for under-resolved molecular dynamics” by A. Bittracher, C. Hartmann, O. Junge and P. Koltai p. 2525

Conference announcements

EPJ

The European Physical Journal Special Topics

Volume 224 / No 12 (2015)

Discussion and Debate: Recurrent Problems in Scale Bridging Techniques in Molecular Simulation – What are the Current Options?

Discussion and Debate: Recurrent Problems in Scale Bridging Techniques in Molecular Simulation – What are the Current Options?

Scale bridging in molecular simulation - Recurrent problems and current options p. 2173

Thermodynamic consistency and other challenges in coarse-graining models p. 2177

A generalized-Yvon-Born-Green method for coarse-grained modeling - Advances, Challenges, and Insight p. 2193

Multiscale molecular dynamics/hydrodynamics implementation of two dimensional “Mercedes Benz” water model p. 2217

Coarse-graining polymer solutions: A critical appraisal of single- and multi-site models p. 2239

Adaptive resolution simulation in equilibrium and beyond p. 2269

Advantages and challenges in coupling an ideal gas to atomistic models in adaptive resolution simulations p. 2289

An introduction to the problem of bridging quantum and classical dynamics p. 2305

Continuum simulations of water flow past fullerene molecules p. 2321

Open boundary molecular dynamics p. 2331

Effective interactions and large deviations in stochastic processes p. 2351

Reactive flows and unproductive cycles for random walks on complex networks p. 2369

Free energies for rare events: Temperature accelerated MD and MC p. 2389

Practical and conceptual path sampling issues p. 2409

Accelerated dynamics: Mathematical foundations and algorithmic improvements p. 2429

A critical appraisal of Markov state models p. 2445

Pseudo generators for under-resolved molecular dynamics p. 2463

Advancements in multi scale modeling: Adaptive resolution simulations and related issues p. 2491

Comments on “Adaptive resolution simulation in equilibrium and beyond” by H. Wang and A. Agarwal p. 2497

Reply to comment by R. Klein on “Adaptive resolution simulation in equilibrium and beyond” p. 2501

Comments on “Advantages and challenges in coupling an ideal gas to atomistic models in adaptive resolution simulations” by K. Kreis, A.C. Fogarty, K. Kremer and R. Potestio p. 2503

Reply to comments by R. Klein on Advantages and challenges in coupling an ideal gas to atomistic models in adaptive resolution simulations p. 2505

Comment on “An introduction to the problem of bridging quantum and classical dynamics” by S. Bonella and G. Ciccotti p. 2507

Comments on “Open boundary molecular dynamics” by R. Delgado-Buscalioni, J. Sablić and M. Praprotnik p. 2509

Reply to comments by R. Klein on “Open boundary molecular dynamics” p. 2511

The trees and the forest - Aims and objectives of molecular dynamics simulations p. 2515

Comments on “Reactive flows and unproductive cycles for random walks on complex networks” by R. Banisch, N. Djurdjevac-Conrad and C. Schütte p. 2519

Comments on “A critical appraisal of Markov state models” by M. Sarich and C. Schütte p. 2521

Comment on “Pseudo generators for under-resolved molecular dynamics” by A. Bittracher, C. Hartmann, O. Junge and P. Koltai p. 2525

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Conference announcements