C8863 Free Energy Calculations

Faculty of Science
Spring 2011
Extent and Intensity
2/0. 2 credit(s) (plus 1 credit for an exam). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).
Teacher(s)
RNDr. Petr Kulhánek, Ph.D. (lecturer)
Guaranteed by
RNDr. Petr Kulhánek, Ph.D.
National Centre for Biomolecular Research – Faculty of Science
Timetable
Fri 13:00–14:50 C04/211
Prerequisites
C7790 Computat. Chem. and Molec. I
Basic level of general, physical and computational chemistry.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
The capacity limit for the course is 30 student(s).
Current registration and enrolment status: enrolled: 0/30, only registered: 0/30, only registered with preference (fields directly associated with the programme): 0/30
fields of study / plans the course is directly associated with
Course objectives
The course is oriented to obtaining basic knowledge about the free energy calculations employing computational chemistry methods. Students will get an overview of available methods, their advantages and drawbacks. Obtained knowledge should be enough for independent solution of real problems from chemistry, supermolecular chemistry and biochemistry.
Syllabus
  • 1. Free Energy and its Relation to Thermochemistry and Kinetics. Experimental Methods of its Measurement. Statistical Physics and Free Energy.
  • 2. Overview of Computational Chemistry. Monte-Carlo versus Molecular Dynamics. Potential Energy Calculations (ab initio, molecular mechanics). Difference between Potential (PES) and Free (FES) Energy Surfaces.
  • 3. Overview of Methods of Free Energy Calculations: End-point Methods, Alchemical Transformations, Potential of Mean Force Methods, Special Methods.
  • 4. End-point Methods. Free Energy from Local Extrema on PES. MM/XXSA (XX=PB,GB,LR). Solvation Free Energy Calculations. Entropy Contribution Calculations.
  • 5. Alchemical Transformations. Free Energy Perturbations (FEP). Thermodynamical Integration (TI). Problems with Atom Anihilation and Creation. Staging versus Sampling.
  • 6. Potential of Mean Force Methods (PMF). Sampling Problem. Adaptive Biasing Force Method. Blue Moon Method. Umbrella Sampling. Metadynamics. Steered Dynamics. Multiple Walkers Approach.
  • 7. Special Methods. Sampling Improving. Replica-Exchange Molecular Dynamics, etc.
Literature
  • Free energy calculations : theory and applications in chemistry a biology. Edited by Christophe Chipot - Andrew Pohorille. Berlin: Springer, 2007, xviii, 517. ISBN 9783540384472. info
  • CRAMER, Christopher J. Essentials of computational chemistry : theories and models. 2nd ed. Chichester: John Wiley & Sons, 2004, xx, 596. ISBN 0470091819. info
  • LEACH, Andrew R. Molecular modelling : principles and applications. 2nd ed. Harlow: Prentice Hall, 2001, xxiii, 744. ISBN 0582382106. info
Teaching methods
presentation, class discussion
Assessment methods
The course is finished by a written test, which is followed by an oral exam.
Language of instruction
Czech
Follow-Up Courses
Further Comments
Study Materials
The course is taught annually.
The course is also listed under the following terms Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019, Spring 2020, Spring 2022, Spring 2023, Spring 2024, Spring 2025.
  • Enrolment Statistics (Spring 2011, recent)
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