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Understanding Molecular Simulations: From Algorithms to Applications Daan Frenkel and Berend Smit The following Case Studies are presented in the book: Appendix : Statistical Errors Case Study 1 : Equation Of State Of The Lennard-Jones Fluid (Nvt) Case Study 2 : Importance Of Detailed Balance Case Study 3 : Why Count The Old Configuration Again? Case Study 4 : Static Properties Of The Lennard-Jones Fluid Case Study 5 : Dynamic Properties Of The Lennard-Jones Fluid Case Study 6 : Algorithms To Calculate The Mean Square Displacement Case Study 7 : Equation Of State Of The Lennard-Jones Fluid (Npt) Case Study 8 : Phase Equilibria From Constant Pressure Simulations Case Study 9 : Equation Of State Of The Lennard-Jones Fluid (Muvt) Case Study 10 : Lennard-Jones: Andersen Thermostat Case Study 11 : Lennard-Jones: Nose-Hoover Thermostat Case Study 12 : Harmonic Oscillator (I) Case Study 13 : Harmonic Oscillator (II) Case Study 14 : Chemical Potential: Widom Method Case Study 15 : Chemical Potential: Overlapping Distribution Case Study 16 : Phase Equilibria Of The Lennard-Jones Fluid Case Study 17 : Solid-Liquid Equilibrium Of Hard Spheres Case Study 18 : Equation Of State Of Lennard-Jones Chains Case Study 19 : Generation Of Trial Configurations Of Ideal Chains Case Study 20 : Recoil Growth Simulation of Lennard-Jones Chains Case Study 21 : Parallel Tempering of a Single Particle Case Study 22 : Multiple Timesteps vs. Constraints Case Study 23 : Ideal Gas Particle Over A Barrier Case Study 24 : Ideal Gas Particle in a Two-dimensional Potential Case Study 25 : Dissipative Particle Dynamics Case Study 26 : Comparison Of Schemes For The Lennard-Jones Fluid Tools : - Random Number Generators In C And Fortran 77 - Random Vector On A Sphere - Gaussian Random Numbers Casestudies 19,20,21,22,23,24 have been written by Thijs J.H. Vlugt; Casestudy 27 written by Thijs J.H. Vlugt and Maddalena Venturoli. Additional material about molecular simulations can be found on the web: http://molsim.chem.uva.nl/course/material.html To compile the source of a Casestudy, simply type "make" in the directory containing the source code. All makefiles have been prepared for RedHat Linux 6.1 (Cartman) on an i386 using the GNU compilers. For other Unix systems, the Makefile may have to be modified. The random number generator provided in this distribution was written in C (ran_uniform.c) for some Casestudies. Some care have to be taken, because some compilers put underscores after FORTRAN77 subroutines. For example, for SGI machines ran_uniform__ has to be changed into ran_uniform_ (see Tools/ran_uniform_SGI.c). We have done our best to remove all errors from this document and the programs. However, we have to make the following statement: We make no warranties, express or implied, that the programs contained in this work are free of error, or that they will meet your requirements for any particular application. They should not be relied on for solving problems whose incorrect solution could results in injury, damage, or loss of property. The authors and publishers disclaim all liability for direct or consequential damages resulting from your use of the programs. If you have any suggestions or remarks, please send them to Berend Smit (bsmit@science.uva.nl). Berend Smit Department of Chemical Engineering University of Amsterdam Nieuwe Achtergracht 166 1018 WV Amsterdam, The Netherlands Email: bsmit@science.uva.nl Homepage: http://molsim.chem.uva.nl Daan Frenkel FOM Institute for Atomic and Molecular Physics Kruislaan 407 10*** SJ Amsterdam Email: frenkel@amolf.nl Homepage: http://www.amolf.nl/research/computational_physics/index.html

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