C–IBI: Targeting cumulative coordination within an iterative protocol to derive coarse-grained models of (multi-component) complex fluids

de Oliveira, Tiago E.; Netz, Paulo A.; Kremer, Kurt; Junghans, Christoph; Mukherji, Debashish

doi:10.1063/1.4947253

Title: C–IBI: Targeting cumulative coordination within an iterative protocol to derive coarse-grained models of (multi-component) complex fluids

Abstract

We present a coarse-graining strategy that we test for aqueous mixtures. The method uses pair-wise cumulative coordination as a target function within an iterative Boltzmann inversion (IBI) like protocol. We name this method coordination iterative Boltzmann inversion (C–IBI). While the underlying coarse-grained model is still structure based and, thus, preserves pair-wise solution structure, our method also reproduces solvation thermodynamics of binary and/or ternary mixtures. In addition, we observe much faster convergence within C–IBI compared to IBI. To validate the robustness, we apply C–IBI to study test cases of solvation thermodynamics of aqueous urea and a triglycine solvation in aqueous urea.

Authors:

de Oliveira, Tiago E. ^[1]; Netz, Paulo A. ^[1]; Kremer, Kurt ^[2];

^[3];

^[2]

Max-Planck Institut fur Polymerforschung, Ackermannweg, Mainz (Germany); Univ. Federal do Rio Grande do Sul, Porto Alegre (Brazil)
Max-Planck Institut fur Polymerforschung, Ackermannweg, Mainz (Germany)
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

Publication Date:: Tue May 03 00:00:00 EDT 2016

Research Org.:: Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)

Sponsoring Org.:: USDOE

OSTI Identifier:: 1260415

Report Number(s):: LA-UR-15-28326
Journal ID: ISSN 0021-9606; JCPSA6

Grant/Contract Number:: AC52-06NA25396

Resource Type:: Journal Article: Accepted Manuscript

Journal Name:: Journal of Chemical Physics

Additional Journal Information:: Journal Volume: 144; Journal Issue: 17; Journal ID: ISSN 0021-9606

Publisher:: American Institute of Physics (AIP)

Country of Publication:: United States

Language:: English

Subject:: 74 ATOMIC AND MOLECULAR PHYSICS; coarse-graining; soft matter; VOTCA; Boltzmann equations; thermodynamic properties; free energy; particle fluctuations; solution thermodynamics

Citation Formats


                    de Oliveira, Tiago E., Netz, Paulo A., Kremer, Kurt, Junghans, Christoph, and Mukherji, Debashish. C–IBI: Targeting cumulative coordination within an iterative protocol to derive coarse-grained models of (multi-component) complex fluids.  United States: N. p., 2016. 
        Web.  doi:10.1063/1.4947253.

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                    de Oliveira, Tiago E., Netz, Paulo A., Kremer, Kurt, Junghans, Christoph, & Mukherji, Debashish. C–IBI: Targeting cumulative coordination within an iterative protocol to derive coarse-grained models of (multi-component) complex fluids.  United States.  https://doi.org/10.1063/1.4947253

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                    de Oliveira, Tiago E., Netz, Paulo A., Kremer, Kurt, Junghans, Christoph, and Mukherji, Debashish. 2016.  
        "C–IBI: Targeting cumulative coordination within an iterative protocol to derive coarse-grained models of (multi-component) complex fluids".  United States.  https://doi.org/10.1063/1.4947253.  https://www.osti.gov/servlets/purl/1260415.

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@article{osti_1260415,

  title        = {C–IBI: Targeting cumulative coordination within an iterative protocol to derive coarse-grained models of (multi-component) complex fluids},

  author       = {de Oliveira, Tiago E. and Netz, Paulo A. and Kremer, Kurt and Junghans, Christoph and Mukherji, Debashish},

  abstractNote = {We present a coarse-graining strategy that we test for aqueous mixtures. The method uses pair-wise cumulative coordination as a target function within an iterative Boltzmann inversion (IBI) like protocol. We name this method coordination iterative Boltzmann inversion (C–IBI). While the underlying coarse-grained model is still structure based and, thus, preserves pair-wise solution structure, our method also reproduces solvation thermodynamics of binary and/or ternary mixtures. In addition, we observe much faster convergence within C–IBI compared to IBI. To validate the robustness, we apply C–IBI to study test cases of solvation thermodynamics of aqueous urea and a triglycine solvation in aqueous urea.},

  doi          = {10.1063/1.4947253},

  url          = {https://www.osti.gov/biblio/1260415},
  journal      = {Journal of Chemical Physics},

  issn         = {0021-9606},

  number       = 17,

  volume       = 144,

  place        = {United States},

  year         = {Tue May 03 00:00:00 EDT 2016},

  month        = {Tue May 03 00:00:00 EDT 2016}

}

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Works referenced in this record:

Multiscale simulation of soft matter systems – from the atomistic to the coarse-grained level and back
journal, January 2009

Peter, Christine; Kremer, Kurt
Soft Matter, Vol. 5, Issue 22
https://doi.org/10.1039/b912027k

Multiscale simulation of soft matter systems
journal, January 2010

Peter, Christine; Kremer, Kurt
Faraday Discuss., Vol. 144
https://doi.org/10.1039/b919800h

Perspective: Coarse-grained models for biomolecular systems
journal, September 2013

Noid, W. G.
The Journal of Chemical Physics, Vol. 139, Issue 9
https://doi.org/10.1063/1.4818908

Interatomic Potentials from First-Principles Calculations: The Force-Matching Method
journal, June 1994

Ercolessi, F.; Adams, J. B.
Europhysics Letters (EPL), Vol. 26, Issue 8
https://doi.org/10.1209/0295-5075/26/8/005

Multiscale coarse graining of liquid-state systems
journal, October 2005

Izvekov, Sergei; Voth, Gregory A.
The Journal of Chemical Physics, Vol. 123, Issue 13
https://doi.org/10.1063/1.2038787

Calculation of effective interaction potentials from radial distribution functions: A reverse Monte Carlo approach
journal, October 1995

Lyubartsev, Alexander P.; Laaksonen, Aatto
Physical Review E, Vol. 52, Issue 4
https://doi.org/10.1103/PhysRevE.52.3730

Systematic hierarchical coarse-graining with the inverse Monte Carlo method
journal, December 2015

Lyubartsev, Alexander P.; Naômé, Aymeric; Vercauteren, Daniel P.
The Journal of Chemical Physics, Vol. 143, Issue 24
https://doi.org/10.1063/1.4934095

Simulation of polymer melts. I. Coarse-graining procedure for polycarbonates
journal, February 1998

Tschöp, W.; Kremer, K.; Batoulis, J.
Acta Polymerica, Vol. 49, Issue 2-3
https://doi.org/10.1002/(SICI)1521-4044(199802)49:2/3<61::AID-APOL61>3.0.CO;2-V

Simulation of polymer melts. II. From coarse-grained models back to atomistic description
journal, February 1998

Tschöp, W.; Kremer, K.; Hahn, O.
Acta Polymerica, Vol. 49, Issue 2-3
https://doi.org/10.1002/(SICI)1521-4044(199802)49:2/3<75::AID-APOL75>3.0.CO;2-5

Deriving effective mesoscale potentials from atomistic simulations: Mesoscale Potentials from Atomistic Simulations
journal, August 2003

Reith, Dirk; Pütz, Mathias; Müller-Plathe, Florian
Journal of Computational Chemistry, Vol. 24, Issue 13
https://doi.org/10.1002/jcc.10307

The relative entropy is fundamental to multiscale and inverse thermodynamic problems
journal, October 2008

Shell, M. Scott
The Journal of Chemical Physics, Vol. 129, Issue 14
https://doi.org/10.1063/1.2992060

Dynamics of Polystyrene Melts through Hierarchical Multiscale Simulations
journal, February 2009

Harmandaris, Vagelis A.; Kremer, Kurt
Macromolecules, Vol. 42, Issue 3
https://doi.org/10.1021/ma8018624

Transferability of Coarse Grained Potentials: Implicit Solvent Models for Hydrated Ions
journal, May 2011

Shen, Jia-Wei; Li, Chunli; van der Vegt, Nico F. A.
Journal of Chemical Theory and Computation, Vol. 7, Issue 6
https://doi.org/10.1021/ct2001396

A transferable coarse-grained model for diphenylalanine: How to represent an environment driven conformational transition
journal, December 2013

Dalgicdir, Cahit; Sensoy, Ozge; Peter, Christine
The Journal of Chemical Physics, Vol. 139, Issue 23
https://doi.org/10.1063/1.4848675

Water Modeled As an Intermediate Element between Carbon and Silicon ^†
journal, April 2009

Molinero, Valeria; Moore, Emily B.
The Journal of Physical Chemistry B, Vol. 113, Issue 13
https://doi.org/10.1021/jp805227c

The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations
journal, July 2007

Marrink, Siewert J.; Risselada, H. Jelger; Yefimov, Serge
The Journal of Physical Chemistry B, Vol. 111, Issue 27
https://doi.org/10.1021/jp071097f

Comparative atomistic and coarse-grained study of water: What do we lose by coarse-graining?
journal, January 2009

Wang, Han; Junghans, Christoph; Kremer, Kurt
The European Physical Journal E, Vol. 28, Issue 2
https://doi.org/10.1140/epje/i2008-10413-5

Bottom-up coarse-grained models that accurately describe the structure, pressure, and compressibility of molecular liquids
journal, December 2015

Dunn, Nicholas J. H.; Noid, W. G.
The Journal of Chemical Physics, Vol. 143, Issue 24
https://doi.org/10.1063/1.4937383

Coil–Globule–Coil Transition of PNIPAm in Aqueous Methanol: Coupling All-Atom Simulations to Semi-Grand Canonical Coarse-Grained Reservoir
journal, November 2013

Mukherji, Debashish; Kremer, Kurt
Macromolecules, Vol. 46, Issue 22
https://doi.org/10.1021/ma401877c

Relative Entropy and Optimization-Driven Coarse-Graining Methods in VOTCA
journal, July 2015

Mashayak, S. Y.; Jochum, Mara N.; Koschke, Konstantin
PLOS ONE, Vol. 10, Issue 7
https://doi.org/10.1371/journal.pone.0131754

Adaptive resolution molecular-dynamics simulation: Changing the degrees of freedom on the fly
journal, December 2005

Praprotnik, Matej; Delle Site, Luigi; Kremer, Kurt
The Journal of Chemical Physics, Vol. 123, Issue 22
https://doi.org/10.1063/1.2132286

Adaptive resolution molecular dynamics simulation through coupling to an internal particle reservoir
journal, April 2012

Fritsch, S.; Poblete, S.; Junghans, C.
Physical Review Letters, Vol. 108, Issue 17
https://doi.org/10.1103/PhysRevLett.108.170602

Kirkwood–Buff Analysis of Liquid Mixtures in an Open Boundary Simulation
journal, February 2012

Mukherji, Debashish; van der Vegt, Nico F. A.; Kremer, Kurt
Journal of Chemical Theory and Computation, Vol. 8, Issue 2
https://doi.org/10.1021/ct200709h

The Statistical Mechanical Theory of Solutions. I
journal, June 1951

Kirkwood, John G.; Buff, Frank P.
The Journal of Chemical Physics, Vol. 19, Issue 6
https://doi.org/10.1063/1.1748352

Preferential Solvation of Triglycine in Aqueous Urea: An Open Boundary Simulation Approach
journal, March 2012

Mukherji, Debashish; van der Vegt, Nico F. A.; Kremer, Kurt
Journal of Chemical Theory and Computation, Vol. 8, Issue 10
https://doi.org/10.1021/ct300253n

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit
journal, February 2013

Pronk, Sander; Páll, Szilárd; Schulz, Roland
Bioinformatics, Vol. 29, Issue 7
https://doi.org/10.1093/bioinformatics/btt055

A Kirkwood−Buff Derived Force Field for Mixtures of Urea and Water
journal, April 2003

Weerasinghe, Samantha; Smith, Paul E.
The Journal of Physical Chemistry B, Vol. 107, Issue 16
https://doi.org/10.1021/jp022049s

The missing term in effective pair potentials
journal, November 1987

Berendsen, H. J. C.; Grigera, J. R.; Straatsma, T. P.
The Journal of Physical Chemistry, Vol. 91, Issue 24
https://doi.org/10.1021/j100308a038

Principles that Govern the Folding of Protein Chains
journal, July 1973

Anfinsen, C. B.
Science, Vol. 181, Issue 4096
https://doi.org/10.1126/science.181.4096.223

Molecular dynamics with coupling to an external bath
journal, October 1984

Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.
The Journal of Chemical Physics, Vol. 81, Issue 8
https://doi.org/10.1063/1.448118

A smooth particle mesh Ewald method
journal, November 1995

Essmann, Ulrich; Perera, Lalith; Berkowitz, Max L.
The Journal of Chemical Physics, Vol. 103, Issue 19
https://doi.org/10.1063/1.470117

LINCS: A linear constraint solver for molecular simulations
journal, September 1997

Hess, Berk; Bekker, Henk; Berendsen, Herman J. C.
Journal of Computational Chemistry, Vol. 18, Issue 12
https://doi.org/10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H

Kirkwood–Buff Coarse-Grained Force Fields for Aqueous Solutions
journal, April 2012

Ganguly, Pritam; Mukherji, Debashish; Junghans, Christoph
Journal of Chemical Theory and Computation, Vol. 8, Issue 5
https://doi.org/10.1021/ct3000958

Representability and Transferability of Kirkwood–Buff Iterative Boltzmann Inversion Models for Multicomponent Aqueous Systems
journal, November 2013

Ganguly, Pritam; van der Vegt, Nico F. A.
Journal of Chemical Theory and Computation, Vol. 9, Issue 12
https://doi.org/10.1021/ct400242r

Derivation of Coarse Grained Models for Multiscale Simulation of Liquid Crystalline Phase Transitions
journal, February 2012

Mukherjee, Biswaroop; Delle Site, Luigi; Kremer, Kurt
The Journal of Physical Chemistry B, Vol. 116, Issue 29
https://doi.org/10.1021/jp212300d

Thermodynamics of aqueous urea solutions
journal, January 1967

Stokes, Rh
Australian Journal of Chemistry, Vol. 20, Issue 10
https://doi.org/10.1071/CH9672087

Activity and Activity Coefficient of Water in Aqueous Solutions and Their Relationships with Solution Structure Parameters
journal, January 1997

Miyawaki, Osato; Saito, Akiko; Matsuo, Takeshi
Bioscience, Biotechnology, and Biochemistry, Vol. 61, Issue 3
https://doi.org/10.1271/bbb.61.466

Predicting the energetics of osmolyte-induced protein folding/unfolding
journal, October 2005

Auton, M.; Bolen, D. W.
Proceedings of the National Academy of Sciences, Vol. 102, Issue 42
https://doi.org/10.1073/pnas.0507053102

VMD: Visual molecular dynamics
journal, February 1996

Humphrey, William; Dalke, Andrew; Schulten, Klaus
Journal of Molecular Graphics, Vol. 14, Issue 1
https://doi.org/10.1016/0263-7855(96)00018-5

Md Simulation Trajectory And Related Files For Dmpc Bilayer, Högberg Et Al, J.Comp.Chem., 29, 2359 (2008)
dataset, January 2015

Lyubartsev, Alexander
Zenodo
https://doi.org/10.5281/zenodo.16195

Works referencing / citing this record:

Adaptive resolution simulation of oligonucleotides
journal, December 2016

Netz, Paulo A.; Potestio, Raffaello; Kremer, Kurt
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journal, September 2019

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The Journal of Chemical Physics, Vol. 151, Issue 12
https://doi.org/10.1063/1.5097559

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journal, October 2016

Rosenberger, David; Hanke, Martin; van der Vegt, Nico F. A.
The European Physical Journal Special Topics, Vol. 225, Issue 8-9
https://doi.org/10.1140/epjst/e2016-60120-1

MARTINI-based Coarse-grained Model for Poly(alpha-peptoid)s
preprint, January 2019

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arXiv
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Title: C–IBI: Targeting cumulative coordination within an iterative protocol to derive coarse-grained models of (multi-component) complex fluids

Abstract

Citation Formats

Multiscale simulation of soft matter systems – from the atomistic to the coarse-grained level and back journal, January 2009

Multiscale simulation of soft matter systems journal, January 2010

Perspective: Coarse-grained models for biomolecular systems journal, September 2013

Interatomic Potentials from First-Principles Calculations: The Force-Matching Method journal, June 1994

Multiscale coarse graining of liquid-state systems journal, October 2005

Calculation of effective interaction potentials from radial distribution functions: A reverse Monte Carlo approach journal, October 1995

Systematic hierarchical coarse-graining with the inverse Monte Carlo method journal, December 2015

Simulation of polymer melts. I. Coarse-graining procedure for polycarbonates journal, February 1998

Simulation of polymer melts. II. From coarse-grained models back to atomistic description journal, February 1998

Deriving effective mesoscale potentials from atomistic simulations: Mesoscale Potentials from Atomistic Simulations journal, August 2003

The relative entropy is fundamental to multiscale and inverse thermodynamic problems journal, October 2008

Dynamics of Polystyrene Melts through Hierarchical Multiscale Simulations journal, February 2009

Transferability of Coarse Grained Potentials: Implicit Solvent Models for Hydrated Ions journal, May 2011

A transferable coarse-grained model for diphenylalanine: How to represent an environment driven conformational transition journal, December 2013

Water Modeled As an Intermediate Element between Carbon and Silicon † journal, April 2009

The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations journal, July 2007

Comparative atomistic and coarse-grained study of water: What do we lose by coarse-graining? journal, January 2009

Bottom-up coarse-grained models that accurately describe the structure, pressure, and compressibility of molecular liquids journal, December 2015

Coil–Globule–Coil Transition of PNIPAm in Aqueous Methanol: Coupling All-Atom Simulations to Semi-Grand Canonical Coarse-Grained Reservoir journal, November 2013

Relative Entropy and Optimization-Driven Coarse-Graining Methods in VOTCA journal, July 2015

Adaptive resolution molecular-dynamics simulation: Changing the degrees of freedom on the fly journal, December 2005

Adaptive resolution molecular dynamics simulation through coupling to an internal particle reservoir journal, April 2012

Kirkwood–Buff Analysis of Liquid Mixtures in an Open Boundary Simulation journal, February 2012

The Statistical Mechanical Theory of Solutions. I journal, June 1951

Preferential Solvation of Triglycine in Aqueous Urea: An Open Boundary Simulation Approach journal, March 2012

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit journal, February 2013

A Kirkwood−Buff Derived Force Field for Mixtures of Urea and Water journal, April 2003

The missing term in effective pair potentials journal, November 1987

Principles that Govern the Folding of Protein Chains journal, July 1973

Molecular dynamics with coupling to an external bath journal, October 1984

A smooth particle mesh Ewald method journal, November 1995

LINCS: A linear constraint solver for molecular simulations journal, September 1997

Kirkwood–Buff Coarse-Grained Force Fields for Aqueous Solutions journal, April 2012

Representability and Transferability of Kirkwood–Buff Iterative Boltzmann Inversion Models for Multicomponent Aqueous Systems journal, November 2013

Derivation of Coarse Grained Models for Multiscale Simulation of Liquid Crystalline Phase Transitions journal, February 2012

Thermodynamics of aqueous urea solutions journal, January 1967

Activity and Activity Coefficient of Water in Aqueous Solutions and Their Relationships with Solution Structure Parameters journal, January 1997

Predicting the energetics of osmolyte-induced protein folding/unfolding journal, October 2005

VMD: Visual molecular dynamics journal, February 1996

Md Simulation Trajectory And Related Files For Dmpc Bilayer, Högberg Et Al, J.Comp.Chem., 29, 2359 (2008) dataset, January 2015

Adaptive resolution simulation of oligonucleotides journal, December 2016

Adversarial-residual-coarse-graining: Applying machine learning theory to systematic molecular coarse-graining journal, September 2019

Comparison of iterative inverse coarse-graining methods journal, October 2016

MARTINI-based Coarse-grained Model for Poly(alpha-peptoid)s preprint, January 2019

Multiscale simulation of soft matter systems – from the atomistic to the coarse-grained level and back
journal, January 2009

Multiscale simulation of soft matter systems
journal, January 2010

Perspective: Coarse-grained models for biomolecular systems
journal, September 2013

Interatomic Potentials from First-Principles Calculations: The Force-Matching Method
journal, June 1994

Multiscale coarse graining of liquid-state systems
journal, October 2005

Calculation of effective interaction potentials from radial distribution functions: A reverse Monte Carlo approach
journal, October 1995

Systematic hierarchical coarse-graining with the inverse Monte Carlo method
journal, December 2015

Simulation of polymer melts. I. Coarse-graining procedure for polycarbonates
journal, February 1998

Simulation of polymer melts. II. From coarse-grained models back to atomistic description
journal, February 1998

Deriving effective mesoscale potentials from atomistic simulations: Mesoscale Potentials from Atomistic Simulations
journal, August 2003

The relative entropy is fundamental to multiscale and inverse thermodynamic problems
journal, October 2008

Dynamics of Polystyrene Melts through Hierarchical Multiscale Simulations
journal, February 2009

Transferability of Coarse Grained Potentials: Implicit Solvent Models for Hydrated Ions
journal, May 2011

A transferable coarse-grained model for diphenylalanine: How to represent an environment driven conformational transition
journal, December 2013

Water Modeled As an Intermediate Element between Carbon and Silicon ^†
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journal, July 2007

Comparative atomistic and coarse-grained study of water: What do we lose by coarse-graining?
journal, January 2009

Bottom-up coarse-grained models that accurately describe the structure, pressure, and compressibility of molecular liquids
journal, December 2015

Coil–Globule–Coil Transition of PNIPAm in Aqueous Methanol: Coupling All-Atom Simulations to Semi-Grand Canonical Coarse-Grained Reservoir
journal, November 2013

Relative Entropy and Optimization-Driven Coarse-Graining Methods in VOTCA
journal, July 2015

Adaptive resolution molecular-dynamics simulation: Changing the degrees of freedom on the fly
journal, December 2005

Adaptive resolution molecular dynamics simulation through coupling to an internal particle reservoir
journal, April 2012

Kirkwood–Buff Analysis of Liquid Mixtures in an Open Boundary Simulation
journal, February 2012

The Statistical Mechanical Theory of Solutions. I
journal, June 1951

Preferential Solvation of Triglycine in Aqueous Urea: An Open Boundary Simulation Approach
journal, March 2012

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit
journal, February 2013

A Kirkwood−Buff Derived Force Field for Mixtures of Urea and Water
journal, April 2003

The missing term in effective pair potentials
journal, November 1987

Principles that Govern the Folding of Protein Chains
journal, July 1973

Molecular dynamics with coupling to an external bath
journal, October 1984

A smooth particle mesh Ewald method
journal, November 1995

LINCS: A linear constraint solver for molecular simulations
journal, September 1997

Kirkwood–Buff Coarse-Grained Force Fields for Aqueous Solutions
journal, April 2012

Representability and Transferability of Kirkwood–Buff Iterative Boltzmann Inversion Models for Multicomponent Aqueous Systems
journal, November 2013

Derivation of Coarse Grained Models for Multiscale Simulation of Liquid Crystalline Phase Transitions
journal, February 2012

Thermodynamics of aqueous urea solutions
journal, January 1967

Activity and Activity Coefficient of Water in Aqueous Solutions and Their Relationships with Solution Structure Parameters
journal, January 1997

Predicting the energetics of osmolyte-induced protein folding/unfolding
journal, October 2005

VMD: Visual molecular dynamics
journal, February 1996

Md Simulation Trajectory And Related Files For Dmpc Bilayer, Högberg Et Al, J.Comp.Chem., 29, 2359 (2008)
dataset, January 2015

Adaptive resolution simulation of oligonucleotides
journal, December 2016

Adversarial-residual-coarse-graining: Applying machine learning theory to systematic molecular coarse-graining
journal, September 2019

Comparison of iterative inverse coarse-graining methods
journal, October 2016

MARTINI-based Coarse-grained Model for Poly(alpha-peptoid)s
preprint, January 2019