Matej Praprotnik

发表

Molecular Dynamics Integration Time Step Dependence of the Split Integration Symplectic Method on System Density

Dusanka Janezic, Matej Praprotnik, 2003, J. Chem. Inf. Comput. Sci..

STOCK: Structure mapper and online coarse‐graining kit for molecular simulations

Matej Praprotnik, Stas Bevc, Christoph Junghans, 2014, J. Comput. Chem..

Multiscale Simulation of Protein Hydration Using the SWINGER Dynamical Clustering Algorithm.

Matej Praprotnik, Julija Zavadlav, Siewert J Marrink, 2018, Journal of chemical theory and computation.

Multiscale simulation of soft matter: from scale bridging to adaptive resolution.

Matej Praprotnik, Kurt Kremer, Luigi Delle Site, 2008, Annual review of physical chemistry.

Parallel Approaches in Molecular Dynamics Simulations

Matej Praprotnik, Urban Borštnik, Dušanka Janežič, 2009 .

ENZO: A Web Tool for Derivation and Evaluation of Kinetic Models of Enzyme Catalyzed Reactions

Matej Praprotnik, Milan Hodošček, Dušanka Janežič, 2011, PloS one.

Simulation approaches to soft matter: Generic statistical properties vs. chemical details

Matej Praprotnik, Kurt Kremer, Christoph Junghans, 2008, Comput. Phys. Commun..

Adaptive resolution simulation of liquid water

Matej Praprotnik, Cecilia Clementi, Kurt Kremer, 2007 .

Adaptive Resolution Schemes

Matej Praprotnik, Luigi Delle Site, C. Junghans, 2009 .

Adaptive Resolution in Molecular Dynamics Simulations

Matej Praprotnik, Cecilia Clementi, Kurt Kremer, 2007 .

Multiscale simulation of water flow past a C540 fullerene

Matej Praprotnik, Petros Koumoutsakos, Jens H. Walther, 2012, J. Comput. Phys..

Adaptive Resolution Simulation of MARTINI Solvents.

Matej Praprotnik, Julija Zavadlav, Siewert J Marrink, 2014, Journal of chemical theory and computation.

New all‐atom force field for molecular dynamics simulation of an AlPO4‐34 molecular sieve

Dusanka Janezic, Matej Praprotnik, Milan Hodoscek, 2008, J. Comput. Chem..

Molecular Dynamics Integration Meets Standard Theory of Molecular Vibrations

Dusanka Janezic, Matej Praprotnik, 2005, J. Chem. Inf. Model..

Molecular Dynamics Simulation of High Density DNA Arrays

Matej Praprotnik, Julija Zavadlav, Rudolf Podgornik, 2018, Comput..

Modeling diffusive dynamics in adaptive resolution simulation of liquid water.

Matej Praprotnik, Cecilia Clementi, Kurt Kremer, 2007, The Journal of chemical physics.

Coupling different levels of resolution in molecular simulations.

Matej Praprotnik, Kurt Kremer, Simón Poblete, 2009, The Journal of chemical physics.

The split integration symplectic method.

Dusanka Janezic, Matej Praprotnik, 2002, Cellular & molecular biology letters.

Concurrent triple-scale simulation of molecular liquids.

Matej Praprotnik, Rafael Delgado-Buscalioni, Kurt Kremer, 2008, The Journal of chemical physics.

Adaptive resolution simulation of an atomistic protein in MARTINI water.

Matej Praprotnik, Julija Zavadlav, Siewert J Marrink, 2014, The Journal of chemical physics.

SWINGER: a clustering algorithm for concurrent coupling of atomistic and supramolecular liquids

Matej Praprotnik, Julija Zavadlav, Siewert J. Marrink, 2019, Interface Focus.

FAST TRACK COMMUNICATION: Fractional dimensions of phase space variables: a tool for varying the degrees of freedom of a system in a multiscale treatment

Matej Praprotnik, Kurt Kremer, Luigi Delle Site, 2007 .

Coupling atomistic and continuum hydrodynamics through a mesoscopic model: application to liquid water.

Matej Praprotnik, Rafael Delgado-Buscalioni, Kurt Kremer, 2009, The Journal of chemical physics.

Molecular dynamics integration and molecular vibrational theory. II. Simulation of nonlinear molecules.

Dusanka Janezic, Matej Praprotnik, D. Janežič, 2005, The Journal of chemical physics.

Symplectic molecular dynamics integration using normal mode analysis

Matej Praprotnik, Dušanka Janežič, D. Janežič, 2001 .

Transport properties controlled by a thermostat: An extended dissipative particle dynamics thermostat.

Matej Praprotnik, Kurt Kremer, Christoph Junghans, 2007, Soft matter.

Open boundary molecular dynamics of sheared star-polymer melts.

Matej Praprotnik, Rafael Delgado-Buscalioni, M. Praprotnik, 2016, Soft matter.

Molecular systems with open boundaries: Theory and simulation

Matej Praprotnik, Luigi Delle Site, M. Praprotnik, 2017 .

A macromolecule in a solvent: adaptive resolution molecular dynamics simulation.

Matej Praprotnik, Kurt Kremer, Luigi Delle Site, 2007, The Journal of chemical physics.

Temperature Dependence of Water Vibrational Spectrum: A Molecular Dynamics Simulation Study

Dusanka Janezic, Matej Praprotnik, Janez Mavri, 2004 .

Adaptive molecular resolution via a continuous change of the phase space dimensionality.

Matej Praprotnik, Kurt Kremer, Luigi Delle Site, 2007, Physical review. E, Statistical, nonlinear, and soft matter physics.

Statistical Physics Problems in Adaptive Resolution Computer Simulations of Complex Fluids

Matej Praprotnik, Kurt Kremer, Simón Poblete, 2011 .

INHOMOGENEOUS HEAT-CONDUCTION PROBLEMS SOLVED BY A NEW EXPLICIT FINITE DIFFERENCE SCHEME

Matej Praprotnik, Roman Trobec, R. Trobec, 2004 .

Molecular dynamics integration and molecular vibrational theory. I. New symplectic integrators.

Dusanka Janezic, Matej Praprotnik, Franci Merzel, 2005, The Journal of chemical physics.

Adaptive resolution simulation of a DNA molecule in salt solution.

Matej Praprotnik, Julija Zavadlav, Rudolf Podgornik, 2015, Journal of chemical theory and computation.

Adaptive resolution scheme for efficient hybrid atomistic-mesoscale molecular dynamics simulations of dense liquids.

Matej Praprotnik, Kurt Kremer, Luigi Delle Site, 2006, Physical review. E, Statistical, nonlinear, and soft matter physics.

Adaptive resolution simulation of an atomistic DNA molecule in MARTINI salt solution

Matej Praprotnik, Julija Zavadlav, Rudolf Podgornik, 2016, The European Physical Journal Special Topics.

Adaptive resolution simulation of polarizable supramolecular coarse-grained water models.

Matej Praprotnik, Julija Zavadlav, Siewert J Marrink, 2015, The Journal of chemical physics.