C8862 Free Energy Calculations - Excercise

Faculty of Science
Spring 2020
Extent and Intensity
0/1. 1 credit(s). Type of Completion: z (credit).
Teacher(s)
RNDr. Petr Kulhánek, Ph.D. (lecturer)
Guaranteed by
RNDr. Petr Kulhánek, Ph.D.
National Centre for Biomolecular Research – Faculty of Science
Supplier department: National Centre for Biomolecular Research – Faculty of Science
Timetable
Mon 10:00–10:50 C04/118
Prerequisites
C2110 UNIX and programming && C7800 Comp. Chem. & MM I sem && NOW( C8863 Free Energy Calculations )
Basic level of general, physical, computational chemistry and UNIX type operating system.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
there are 20 fields of study the course is directly associated with, display
Course objectives
The course is oriented to obtaining basic knowledge about the free energy calculations employing computational chemistry methods. Students will exercise selected methods from the course on model systems.
Learning outcomes
Student will be able to:
- choose a suitable method for calculating free energy;
- determine the composition of the reaction mixture in equilibrium;
- design appropriate thermodynamic cycles;
- describe chemical transformations by potential of mean force;
Syllabus
  • free energy by end-point methods
  • solvation free energy by thermodynamic integration
  • free energy of conformational changes by potential of mean force methods
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
practical exercising
Assessment methods
Fulfilling requirements are to finish a project and its defense.
Language of instruction
Czech
Further comments (probably available only in Czech)
Study Materials
The course is taught annually.
General note: v roce 2014 bude výuka probíhat blokově.
The course is also listed under the following terms Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019.

C8862 Free Energy Calculations - Excercise

Faculty of Science
Spring 2019
Extent and Intensity
0/1. 1 credit(s). Type of Completion: z (credit).
Teacher(s)
RNDr. Petr Kulhánek, Ph.D. (lecturer)
Guaranteed by
RNDr. Petr Kulhánek, Ph.D.
National Centre for Biomolecular Research – Faculty of Science
Supplier department: National Centre for Biomolecular Research – Faculty of Science
Timetable
Mon 18. 2. to Fri 17. 5. Tue 11:00–11:50 C04/118
Prerequisites
C2110 UNIX and programming && C7800 Comp. Chem. & MM I sem && NOW( C8863 Free Energy Calculations )
Basic level of general, physical, computational chemistry and UNIX type operating system.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
there are 20 fields of study the course is directly associated with, display
Course objectives
The course is oriented to obtaining basic knowledge about the free energy calculations employing computational chemistry methods. Students will exercise selected methods from the course on model systems.
Syllabus
  • free energy by end-point methods
  • solvation free energy by thermodynamic integration
  • free energy of conformational changes by potential of mean force methods
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
practical exercising
Assessment methods
Fulfilling requirements are to finish a project and its defense.
Language of instruction
Czech
Further comments (probably available only in Czech)
Study Materials
The course is taught annually.
General note: v roce 2014 bude výuka probíhat blokově.
The course is also listed under the following terms Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2020.

C8862 Free Energy Calculations - Excercise

Faculty of Science
spring 2018
Extent and Intensity
0/1. 1 credit(s). Type of Completion: z (credit).
Teacher(s)
RNDr. Petr Kulhánek, Ph.D. (lecturer)
Guaranteed by
RNDr. Petr Kulhánek, Ph.D.
National Centre for Biomolecular Research – Faculty of Science
Supplier department: National Centre for Biomolecular Research – Faculty of Science
Timetable
Mon 10:00–10:50 C04/118
Prerequisites
C2110 UNIX and programming && C7800 Comp. Chem. & MM I sem && NOW( C8863 Free Energy Calculations )
Basic level of general, physical, computational chemistry and UNIX type operating system.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
there are 20 fields of study the course is directly associated with, display
Course objectives
The course is oriented to obtaining basic knowledge about the free energy calculations employing computational chemistry methods. Students will exercise selected methods from the course on model systems.
Syllabus
  • free energy by end-point methods
  • solvation free energy by thermodynamic integration
  • free energy of conformational changes by potential of mean force methods
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
practical exercising
Assessment methods
Fulfilling requirements are to finish a project and its defense.
Language of instruction
Czech
Further comments (probably available only in Czech)
The course is taught annually.
General note: v roce 2014 bude výuka probíhat blokově.
The course is also listed under the following terms Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, Spring 2019, Spring 2020.

C8862 Free Energy Calculations - Excercise

Faculty of Science
Spring 2017
Extent and Intensity
0/1. 1 credit(s). Type of Completion: z (credit).
Teacher(s)
RNDr. Petr Kulhánek, Ph.D. (lecturer)
Guaranteed by
RNDr. Petr Kulhánek, Ph.D.
National Centre for Biomolecular Research – Faculty of Science
Supplier department: National Centre for Biomolecular Research – Faculty of Science
Timetable
Mon 20. 2. to Mon 22. 5. Mon 8:00–8:50 C04/118
Prerequisites
C2110 UNIX and programming && C7800 Comp. Chem. & MM I sem && NOW( C8863 Free Energy Calculations )
Basic level of general, physical, computational chemistry and UNIX type operating system.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
there are 20 fields of study the course is directly associated with, display
Course objectives
The course is oriented to obtaining basic knowledge about the free energy calculations employing computational chemistry methods. Students will exercise selected methods from the course on model systems.
Syllabus
  • free energy by end-point methods
  • solvation free energy by thermodynamic integration
  • free energy of conformational changes by potential of mean force methods
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
practical exercising
Assessment methods
Fulfilling requirements are to finish a project and its defense.
Language of instruction
Czech
Further comments (probably available only in Czech)
The course is taught annually.
General note: v roce 2014 bude výuka probíhat blokově.
The course is also listed under the following terms Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, spring 2018, Spring 2019, Spring 2020.

C8862 Free Energy Calculations - Excercise

Faculty of Science
Spring 2016
Extent and Intensity
0/1. 1 credit(s). Type of Completion: z (credit).
Teacher(s)
RNDr. Petr Kulhánek, Ph.D. (lecturer)
Guaranteed by
RNDr. Petr Kulhánek, Ph.D.
National Centre for Biomolecular Research – Faculty of Science
Supplier department: National Centre for Biomolecular Research – Faculty of Science
Timetable
Mon 10:00–10:50 C04/118
Prerequisites
C2110 UNIX and programming && C7800 Comp. Chem. & MM I sem && NOW( C8863 Free Energy Calculations )
Basic level of general, physical, computational chemistry and UNIX type operating system.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
there are 20 fields of study the course is directly associated with, display
Course objectives
The course is oriented to obtaining basic knowledge about the free energy calculations employing computational chemistry methods. Students will exercise selected methods from the course on model systems.
Syllabus
  • free energy by end-point methods
  • solvation free energy by thermodynamic integration
  • free energy of conformational changes by potential of mean force methods
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
practical exercising
Assessment methods
Fulfilling requirements are to finish a project and its defense.
Language of instruction
Czech
Further comments (probably available only in Czech)
The course is taught annually.
General note: v roce 2014 bude výuka probíhat blokově.
The course is also listed under the following terms Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2017, spring 2018, Spring 2019, Spring 2020.

C8862 Free Energy Calculations - Excercise

Faculty of Science
Spring 2015
Extent and Intensity
0/1. 1 credit(s). Type of Completion: z (credit).
Teacher(s)
RNDr. Petr Kulhánek, Ph.D. (lecturer)
Guaranteed by
RNDr. Petr Kulhánek, Ph.D.
National Centre for Biomolecular Research – Faculty of Science
Supplier department: National Centre for Biomolecular Research – Faculty of Science
Prerequisites
C2110 UNIX and programming && C7800 Comp. Chem. & MM I sem && NOW( C8863 Free Energy Calculations )
Basic level of general, physical, computational chemistry and UNIX type operating system.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
there are 20 fields of study the course is directly associated with, display
Course objectives
The course is oriented to obtaining basic knowledge about the free energy calculations employing computational chemistry methods. Students will exercise selected methods from the course on model systems.
Syllabus
  • free energy by end-point methods
  • solvation free energy by thermodynamic integration
  • free energy of conformational changes by potential of mean force methods
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
practical exercising
Assessment methods
Fulfilling requirements are to finish a project and its defense.
Language of instruction
Czech
Further comments (probably available only in Czech)
The course is taught annually.
The course is taught in blocks.
General note: v roce 2014 bude výuka probíhat blokově.
The course is also listed under the following terms Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2016, Spring 2017, spring 2018, Spring 2019, Spring 2020.

C8862 Free Energy Calculations - Excercise

Faculty of Science
Spring 2014
Extent and Intensity
0/1. 1 credit(s). Type of Completion: z (credit).
Teacher(s)
RNDr. Petr Kulhánek, Ph.D. (lecturer)
Guaranteed by
RNDr. Petr Kulhánek, Ph.D.
National Centre for Biomolecular Research – Faculty of Science
Supplier department: National Centre for Biomolecular Research – Faculty of Science
Prerequisites
C2110 UNIX and programming && C7800 Comp. Chem. & MM I sem && NOW( C8863 Free Energy Calculations )
Basic level of general, physical, computational chemistry and UNIX type operating system.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
there are 20 fields of study the course is directly associated with, display
Course objectives
The course is oriented to obtaining basic knowledge about the free energy calculations employing computational chemistry methods. Students will exercise selected methods from the course on model systems.
Syllabus
  • free energy by end-point methods
  • solvation free energy by thermodynamic integration
  • free energy of conformational changes by potential of mean force methods
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
practical exercising
Assessment methods
Fulfilling requirements are to finish a project and its defense.
Language of instruction
Czech
Further comments (probably available only in Czech)
The course is taught annually.
The course is taught in blocks.
General note: v roce 2014 bude výuka probíhat blokově.
The course is also listed under the following terms Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019, Spring 2020.

C8862 Free Energy Calculations - Excercise

Faculty of Science
Spring 2013
Extent and Intensity
0/1. 1 credit(s). Type of Completion: z (credit).
Teacher(s)
RNDr. Petr Kulhánek, Ph.D. (lecturer)
Guaranteed by
RNDr. Petr Kulhánek, Ph.D.
National Centre for Biomolecular Research – Faculty of Science
Supplier department: National Centre for Biomolecular Research – Faculty of Science
Timetable
Wed 18:00–18:50 C04/118
Prerequisites
C2110 UNIX and programming && C7800 Comp. Chem. & MM I sem && NOW( C8863 Free Energy Calculations )
Basic level of general, physical, computational chemistry and UNIX type operating system.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
there are 22 fields of study the course is directly associated with, display
Course objectives
The course is oriented to obtaining basic knowledge about the free energy calculations employing computational chemistry methods. Students will excercise selected methods from the course on model systems.
Syllabus
  • free energy by end-point methods
  • solvation free energy by thermodynamic integration
  • free energy of conformational changes by potential of mean force methods
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
practical exercising
Assessment methods
Fulfilling requirements are to finish a project and its defense.
Language of instruction
Czech
Further Comments
The course is taught annually.
The course is also listed under the following terms Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019, Spring 2020.

C8862 Free Energy Calculations - Excercise

Faculty of Science
Spring 2012
Extent and Intensity
0/1. 1 credit(s). Type of Completion: z (credit).
Teacher(s)
RNDr. Petr Kulhánek, Ph.D. (lecturer)
Guaranteed by
RNDr. Petr Kulhánek, Ph.D.
National Centre for Biomolecular Research – Faculty of Science
Supplier department: National Centre for Biomolecular Research – Faculty of Science
Timetable
Tue 18:00–18:50 C04/118
Prerequisites
C2110 UNIX and programming && C7800 Comp. Chem. & MM I sem && NOW( C8863 Free Energy Calculations )
Basic level of general, physical, computational chemistry and UNIX type operating system.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
there are 22 fields of study the course is directly associated with, display
Course objectives
The course is oriented to obtaining basic knowledge about the free energy calculations employing computational chemistry methods. Students will excercise selected methods from the course on model systems.
Syllabus
  • free energy by end-point methods
  • solvation free energy by thermodynamic integration
  • free energy of conformational changes by potential of mean force methods
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
practical exercising
Assessment methods
Fulfilling requirements are to finish a project and its defense.
Language of instruction
Czech
Further Comments
The course is taught annually.
The course is also listed under the following terms Spring 2011, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019, Spring 2020.

C8862 Free Energy Calculations - Excercise

Faculty of Science
Spring 2011
Extent and Intensity
0/1. 1 credit(s). Type of Completion: z (credit).
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 15:00–16:00 C04/211
Prerequisites
C2110 UNIX and programming && C7800 Comp. Chem. & MM I sem && NOW( C8863 Free Energy Calculations )
Basic level of general, physical, computational chemistry and UNIX type operating system.
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 21 student(s).
Current registration and enrolment status: enrolled: 0/21, only registered: 0/21, only registered with preference (fields directly associated with the programme): 0/21
fields of study / plans the course is directly associated with
there are 22 fields of study the course is directly associated with, display
Course objectives
The course is oriented to obtaining basic knowledge about the free energy calculations employing computational chemistry methods. Students will excercise selected methods from the course on model systems.
Syllabus
  • free energy by end-point methods
  • solvation free energy by thermodynamic integration
  • free energy of conformational changes by potential of mean force methods
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
practical exercising
Assessment methods
Fulfilling requirements are to finish a project and its defense.
Language of instruction
Czech
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.

C8862 Free Energy Calculations - Excercise

Faculty of Science
Spring 2025

The course is not taught in Spring 2025

Extent and Intensity
0/1. 1 credit(s). Type of Completion: z (credit).
Teacher(s)
RNDr. Petr Kulhánek, Ph.D. (lecturer)
Guaranteed by
RNDr. Petr Kulhánek, Ph.D.
National Centre for Biomolecular Research – Faculty of Science
Supplier department: National Centre for Biomolecular Research – Faculty of Science
Prerequisites
C2110 UNIX and Programming && C7800 Intro. to Mol. Mod. - Exerc. && NOW( C8863 Free Energy Calculations )
Basic level of general, physical, computational chemistry and UNIX type operating system.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
there are 20 fields of study the course is directly associated with, display
Course objectives
The course is oriented to obtaining basic knowledge about the free energy calculations employing computational chemistry methods. Students will exercise selected methods from the course on model systems.
Learning outcomes
Student will be able to:
- choose a suitable method for calculating free energy;
- determine the composition of the reaction mixture in equilibrium;
- design appropriate thermodynamic cycles;
- describe chemical transformations by potential of mean force;
Syllabus
  • free energy by end-point methods
  • solvation free energy by thermodynamic integration
  • free energy of conformational changes by potential of mean force methods
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
practical exercising
Assessment methods
Fulfilling requirements are to finish a project and its defense.
Language of instruction
Czech
Further comments (probably available only in Czech)
The course is taught annually.
The course is taught in blocks.
General note: v roce 2014 bude výuka probíhat blokově.
The course is also listed under the following terms Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019, Spring 2020.

C8862 Free Energy Calculations - Excercise

Faculty of Science
Spring 2024

The course is not taught in Spring 2024

Extent and Intensity
0/1. 1 credit(s). Type of Completion: z (credit).
Teacher(s)
RNDr. Petr Kulhánek, Ph.D. (lecturer)
Guaranteed by
RNDr. Petr Kulhánek, Ph.D.
National Centre for Biomolecular Research – Faculty of Science
Supplier department: National Centre for Biomolecular Research – Faculty of Science
Prerequisites
C2110 UNIX and Programming && C7800 Intro. to Mol. Mod. - Exerc. && NOW( C8863 Free Energy Calculations )
Basic level of general, physical, computational chemistry and UNIX type operating system.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
there are 20 fields of study the course is directly associated with, display
Course objectives
The course is oriented to obtaining basic knowledge about the free energy calculations employing computational chemistry methods. Students will exercise selected methods from the course on model systems.
Learning outcomes
Student will be able to:
- choose a suitable method for calculating free energy;
- determine the composition of the reaction mixture in equilibrium;
- design appropriate thermodynamic cycles;
- describe chemical transformations by potential of mean force;
Syllabus
  • free energy by end-point methods
  • solvation free energy by thermodynamic integration
  • free energy of conformational changes by potential of mean force methods
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
practical exercising
Assessment methods
Fulfilling requirements are to finish a project and its defense.
Language of instruction
Czech
Further comments (probably available only in Czech)
The course is taught annually.
The course is taught in blocks.
General note: v roce 2014 bude výuka probíhat blokově.
The course is also listed under the following terms Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019, Spring 2020.

C8862 Free Energy Calculations - Excercise

Faculty of Science
Spring 2023

The course is not taught in Spring 2023

Extent and Intensity
0/1. 1 credit(s). Type of Completion: z (credit).
Teacher(s)
RNDr. Petr Kulhánek, Ph.D. (lecturer)
Guaranteed by
RNDr. Petr Kulhánek, Ph.D.
National Centre for Biomolecular Research – Faculty of Science
Supplier department: National Centre for Biomolecular Research – Faculty of Science
Prerequisites
C2110 UNIX and Programming && C7800 Intro. to Mol. Mod. - Exerc. && NOW( C8863 Free Energy Calculations )
Basic level of general, physical, computational chemistry and UNIX type operating system.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
there are 20 fields of study the course is directly associated with, display
Course objectives
The course is oriented to obtaining basic knowledge about the free energy calculations employing computational chemistry methods. Students will exercise selected methods from the course on model systems.
Learning outcomes
Student will be able to:
- choose a suitable method for calculating free energy;
- determine the composition of the reaction mixture in equilibrium;
- design appropriate thermodynamic cycles;
- describe chemical transformations by potential of mean force;
Syllabus
  • free energy by end-point methods
  • solvation free energy by thermodynamic integration
  • free energy of conformational changes by potential of mean force methods
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
practical exercising
Assessment methods
Fulfilling requirements are to finish a project and its defense.
Language of instruction
Czech
Further comments (probably available only in Czech)
The course is taught annually.
The course is taught in blocks.
General note: v roce 2014 bude výuka probíhat blokově.
The course is also listed under the following terms Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019, Spring 2020.

C8862 Free Energy Calculations - Excercise

Faculty of Science
Spring 2022

The course is not taught in Spring 2022

Extent and Intensity
0/1. 1 credit(s). Type of Completion: z (credit).
Teacher(s)
RNDr. Petr Kulhánek, Ph.D. (lecturer)
Guaranteed by
RNDr. Petr Kulhánek, Ph.D.
National Centre for Biomolecular Research – Faculty of Science
Supplier department: National Centre for Biomolecular Research – Faculty of Science
Prerequisites
C2110 UNIX and Programming && C7800 Intro. to Mol. Mod. - Exerc. && NOW( C8863 Free Energy Calculations )
Basic level of general, physical, computational chemistry and UNIX type operating system.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
there are 20 fields of study the course is directly associated with, display
Course objectives
The course is oriented to obtaining basic knowledge about the free energy calculations employing computational chemistry methods. Students will exercise selected methods from the course on model systems.
Learning outcomes
Student will be able to:
- choose a suitable method for calculating free energy;
- determine the composition of the reaction mixture in equilibrium;
- design appropriate thermodynamic cycles;
- describe chemical transformations by potential of mean force;
Syllabus
  • free energy by end-point methods
  • solvation free energy by thermodynamic integration
  • free energy of conformational changes by potential of mean force methods
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
practical exercising
Assessment methods
Fulfilling requirements are to finish a project and its defense.
Language of instruction
Czech
Further comments (probably available only in Czech)
The course is taught annually.
The course is taught in blocks.
General note: v roce 2014 bude výuka probíhat blokově.
The course is also listed under the following terms Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019, Spring 2020.

C8862 Free Energy Calculations - Excercise

Faculty of Science
Spring 2021

The course is not taught in Spring 2021

Extent and Intensity
0/1. 1 credit(s). Type of Completion: z (credit).
Teacher(s)
RNDr. Petr Kulhánek, Ph.D. (lecturer)
Guaranteed by
RNDr. Petr Kulhánek, Ph.D.
National Centre for Biomolecular Research – Faculty of Science
Supplier department: National Centre for Biomolecular Research – Faculty of Science
Prerequisites
C2110 UNIX and programming && C7800 Comp. Chem. & MM I sem && NOW( C8863 Free Energy Calculations )
Basic level of general, physical, computational chemistry and UNIX type operating system.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
there are 20 fields of study the course is directly associated with, display
Course objectives
The course is oriented to obtaining basic knowledge about the free energy calculations employing computational chemistry methods. Students will exercise selected methods from the course on model systems.
Learning outcomes
Student will be able to:
- choose a suitable method for calculating free energy;
- determine the composition of the reaction mixture in equilibrium;
- design appropriate thermodynamic cycles;
- describe chemical transformations by potential of mean force;
Syllabus
  • free energy by end-point methods
  • solvation free energy by thermodynamic integration
  • free energy of conformational changes by potential of mean force methods
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
practical exercising
Assessment methods
Fulfilling requirements are to finish a project and its defense.
Language of instruction
Czech
Further comments (probably available only in Czech)
The course is taught annually.
The course is taught in blocks.
General note: v roce 2014 bude výuka probíhat blokově.
The course is also listed under the following terms Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019, Spring 2020.

C8862 Free Energy Calculations - Excercise

Faculty of Science
spring 2012 - acreditation

The information about the term spring 2012 - acreditation is not made public

Extent and Intensity
0/1. 1 credit(s). Type of Completion: z (credit).
Teacher(s)
RNDr. Petr Kulhánek, Ph.D. (lecturer)
Guaranteed by
RNDr. Petr Kulhánek, Ph.D.
National Centre for Biomolecular Research – Faculty of Science
Supplier department: National Centre for Biomolecular Research – Faculty of Science
Prerequisites
C2110 UNIX and programming && C7800 Comp. Chem. & MM I sem && NOW( C8863 Free Energy Calculations )
Basic level of general, physical, computational chemistry and UNIX type operating system.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
there are 22 fields of study the course is directly associated with, display
Course objectives
The course is oriented to obtaining basic knowledge about the free energy calculations employing computational chemistry methods. Students will excercise selected methods from the course on model systems.
Syllabus
  • free energy by end-point methods
  • solvation free energy by thermodynamic integration
  • free energy of conformational changes by potential of mean force methods
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
practical exercising
Assessment methods
Fulfilling requirements are to finish a project and its defense.
Language of instruction
Czech
Further Comments
The course is taught annually.
The course is taught in blocks.
The course is also listed under the following terms Spring 2011, Spring 2012, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019, Spring 2020.
  • Enrolment Statistics (recent)