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Cutoff Errors in the Ewald Summation Formulae for Point Charge Systems

Abstract Closed formulae for both real and reciprocal space parts of cutoff errors in the Ewald summation method in cubic periodic boundary conditions are derived. Such estimates are useful in tuning… Expand

The Lennard-Jones fluid: an accurate analytic and theoretically-based equation of state

- J. Kolafa, I. Nezbeda
- Chemistry
- 15 September 1994

Abstract A new analytic equation of state for the Lennard-Jones fluid is proposed. The equation is based on a perturbed virial expansion with a theoretically defined temperature-dependent reference… Expand

Accurate equation of state of the hard sphere fluid in stable and metastable regions

- J. Kolafa, S. Labík, A. Malijevský
- Chemistry
- 6 May 2004

New accurate data on the compressibility factor of the hard sphere fluid are obtained by highly optimized molecular dynamics calculations in the range of reduced densities 0.20–1.03. The relative… Expand

THERMAL UNFOLDING OF UNSOLVATED CYTOCHROME C : EXPERIMENT AND MOLECULAR DYNAMICS SIMULATIONS

- Y. Mao, J. Woenckhaus, J. Kolafa, M. Ratner, M. Jarrold
- Chemistry
- 11 March 1999

The thermal unfolding of unsolvated cytochrome c has been examined in the gas phase using ion-mobility measurements. Measurements were performed for the +5, +6, and +7 protonated charge states from… Expand

A classical polarizable model for simulations of water and ice.

- Linda Viererblová, J. Kolafa
- Medicine, Chemistry
- Physical chemistry chemical physics : PCCP
- 2 November 2011

We develop a classical rigid polarizable model of water for molecular simulations of water and ice. The model uses the Rowlinson five-site geometry: oxygen bearing the Lennard-Jones interaction and… Expand

An examination of the five-site potential (TIP5P) for water

- M. Lísal, J. Kolafa, I. Nezbeda
- Chemistry
- 29 October 2002

Parameterization of the five-site model (TIP5P) for water [M. W. Mahoney and W. L. Jorgensen, J. Chem. Phys. 112, 8910 (2000)] has been examined by several computer simulation methods accounting… Expand

Accurate Binding of Sodium and Calcium to a POPC Bilayer by Effective Inclusion of Electronic Polarization.

- Josef Melcr, H. Martinez-Seara, R. Nencini, J. Kolafa, P. Jungwirth, O. H. S. Ollila
- Chemistry, Medicine
- The journal of physical chemistry. B
- 2 April 2018

Binding affinities and stoichiometries of Na+ and Ca2+ ions to phospholipid bilayers are of paramount significance in the properties and functionality of cellular membranes. Current estimates of… Expand

A New Version of the Insertion Particle Method for Determining the Chemical Potential by Monte Carlo Simulation

- I. Nezbeda, J. Kolafa
- Chemistry
- 1 February 1991

Abstract A new version of the test particle method for determining the chemical potential by Monte Carlo simulations is proposed. The method, applicable to any fluid at any density, combines the… Expand

Static Dielectric Constant from Simulations Revisited: Fluctuations or External Field?

- J. Kolafa, Linda Viererblová
- Chemistry, Medicine
- Journal of chemical theory and computation
- 14 March 2014

We compare two methods-the fluctuation formula and the application of an external electric field-for determining the static relative permittivity (static dielectric constant) from molecular… Expand

Calculation of elementary diagrams using a Metropolis-like simulation method

- S. Labík, Hana Gabrielová, J. Kolafa, A. Malijevský
- Mathematics
- 20 April 2003

A method for the evaluation of higher order elementary diagrams is proposed. It utilizes symbolic algebra programming and automatic code generation. The method is used to calculate elementary… Expand

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