Course Information

C7800 Introduction to Molecular Modelling - Exercise

Extent and Intensity

0/1/0. 1 credit(s). Type of Completion: z (credit).
In-person direct teaching

Teacher(s)

RNDr. Petr Kulhánek, Ph.D. (lecturer)
Ing. Tomáš Trnka, Ph.D. (lecturer)
Mgr. Július Zemaník (seminar tutor)

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 18:00–18:50 C04/118

Prerequisites

NOW( C7790 Intro. to Mol. Mod. )
Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. Knowledge of UNIX operation system is advantage.

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: 17/30, 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

there are 13 fields of study the course is directly associated with, display

Course objectives

At the end of the course students should be able to understand and explain how to use one of the commonly used modeling software packages.

Learning outcomes

Student will be able to:
- create appropriate models of studied problems;
- perform basic quantum-chemical and molecular-mechanical calculations;
- calculate interaction energy;
- find the transition state of the elementary reaction and determine its activation energy;
- describe the dynamics of small molecular system;

Syllabus

• 1. Introduction to Gaussian program - http://www.gaussian.com/ (input data preparation, results analysis and their visualization - Molden, Molekel, VMD)
• 2. Introduction to Amber program package - http://ambermd.org/ (preparation of studied system, equilibration, dynamics, results analysis and their visualization - VMD)
• 3. Elaboration of independent projects

Literature

• LEACH, Andrew R. Molecular modelling : principles and applications. 2nd ed. Harlow: Prentice Hall, 2001, xxiii, 744. ISBN 0582382106. info
• CRAMER, Christopher J. Essentials of computational chemistry : theories and models. 2nd ed. Chichester: John Wiley & Sons, 2004, xx, 596. ISBN 0470091819. info
• JENSEN, Frank. Introduction to computational chemistry. 2nd ed. Chichester: John Wiley & Sons, 2007, xx, 599. ISBN 9780470011874. info
• REMKO, Milan. Molekulové modelovanie :princípy a aplikácie. Bratislava: Slovak Academic Press, 2000, 239 s. ISBN 80-88908-62-0. 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 can also be completed outside the examination period.
The course is taught annually.

C7800 Introduction to Molecular Modelling - Exercise

Extent and Intensity

0/1/0. 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 18:00–18:50 C04/118

Prerequisites

NOW( C7790 Intro. to Mol. Mod. )
Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. Knowledge of UNIX operation system is advantage.

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: 15/30, 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

there are 13 fields of study the course is directly associated with, display

Course objectives

At the end of the course students should be able to understand and explain how to use one of the commonly used modeling software packages.

Learning outcomes

Student will be able to:
- create appropriate models of studied problems;
- perform basic quantum-chemical and molecular-mechanical calculations;
- calculate interaction energy;
- find the transition state of the elementary reaction and determine its activation energy;
- describe the dynamics of small molecular system;

Syllabus

• 1. Introduction to Gaussian program - http://www.gaussian.com/ (input data preparation, results analysis and their visualization - Molden, Molekel, VMD)
• 2. Introduction to Amber program package - http://ambermd.org/ (preparation of studied system, equilibration, dynamics, results analysis and their visualization - VMD)
• 3. Elaboration of independent projects

Literature

• LEACH, Andrew R. Molecular modelling : principles and applications. 2nd ed. Harlow: Prentice Hall, 2001, xxiii, 744. ISBN 0582382106. info
• CRAMER, Christopher J. Essentials of computational chemistry : theories and models. 2nd ed. Chichester: John Wiley & Sons, 2004, xx, 596. ISBN 0470091819. info
• JENSEN, Frank. Introduction to computational chemistry. 2nd ed. Chichester: John Wiley & Sons, 2007, xx, 599. ISBN 9780470011874. info
• REMKO, Milan. Molekulové modelovanie :princípy a aplikácie. Bratislava: Slovak Academic Press, 2000, 239 s. ISBN 80-88908-62-0. 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 can also be completed outside the examination period.
The course is taught annually.

C7800 Introduction to Molecular Modelling - Exercise

Extent and Intensity

0/1/0. 1 credit(s). Type of Completion: z (credit).

Teacher(s)

RNDr. Petr Kulhánek, Ph.D. (lecturer)
Mgr. Tomáš Bouchal, Ph.D. (seminar tutor)
Mgr. Ivo Durník, Ph.D. (seminar tutor)

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 18:00–18:50 C04/118

Prerequisites

NOW( C7790 Intro. to Mol. Mod. )
Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. Knowledge of UNIX operation system is advantage.

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: 4/30, 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

there are 13 fields of study the course is directly associated with, display

Course objectives

At the end of the course students should be able to understand and explain how to use one of the commonly used modeling software packages.

Learning outcomes

Student will be able to:
- create appropriate models of studied problems;
- perform basic quantum-chemical and molecular-mechanical calculations;
- calculate interaction energy;
- find the transition state of the elementary reaction and determine its activation energy;
- describe the dynamics of small molecular system;

Syllabus

• 1. Introduction to Gaussian program - http://www.gaussian.com/ (input data preparation, results analysis and their visualization - Molden, Molekel, VMD)
• 2. Introduction to Amber program package - http://ambermd.org/ (preparation of studied system, equilibration, dynamics, results analysis and their visualization - VMD)
• 3. Elaboration of independent projects

Literature

• LEACH, Andrew R. Molecular modelling : principles and applications. 2nd ed. Harlow: Prentice Hall, 2001, xxiii, 744. ISBN 0582382106. info
• CRAMER, Christopher J. Essentials of computational chemistry : theories and models. 2nd ed. Chichester: John Wiley & Sons, 2004, xx, 596. ISBN 0470091819. info
• JENSEN, Frank. Introduction to computational chemistry. 2nd ed. Chichester: John Wiley & Sons, 2007, xx, 599. ISBN 9780470011874. info
• REMKO, Milan. Molekulové modelovanie :princípy a aplikácie. Bratislava: Slovak Academic Press, 2000, 239 s. ISBN 80-88908-62-0. 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 can also be completed outside the examination period.
The course is taught annually.

C7800 Introduction to Molecular Modelling - Exercise

Extent and Intensity

0/1/0. 1 credit(s). Type of Completion: z (credit).

Teacher(s)

RNDr. Petr Kulhánek, Ph.D. (lecturer)
Mgr. Tomáš Bouchal, Ph.D. (seminar tutor)
Mgr. Ivo Durník, Ph.D. (seminar tutor)

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 17:00–17:50 C04/118

Prerequisites

NOW( C7790 Intro. to Mol. Mod. )
Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. Knowledge of UNIX operation system is advantage.

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: 3/30, 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

there are 13 fields of study the course is directly associated with, display

Course objectives

At the end of the course students should be able to understand and explain how to use one of the commonly used modeling software packages.

Learning outcomes

Student will be able to:
- create appropriate models of studied problems;
- perform basic quantum-chemical and molecular-mechanical calculations;
- calculate interaction energy;
- find the transition state of the elementary reaction and determine its activation energy;
- describe the dynamics of small molecular system;

Syllabus

• 1. Introduction to Gaussian program - http://www.gaussian.com/ (input data preparation, results analysis and their visualization - Molden, Molekel, VMD)
• 2. Introduction to Amber program package - http://ambermd.org/ (preparation of studied system, equilibration, dynamics, results analysis and their visualization - VMD)
• 3. Elaboration of independent projects

Literature

• LEACH, Andrew R. Molecular modelling : principles and applications. 2nd ed. Harlow: Prentice Hall, 2001, xxiii, 744. ISBN 0582382106. info
• CRAMER, Christopher J. Essentials of computational chemistry : theories and models. 2nd ed. Chichester: John Wiley & Sons, 2004, xx, 596. ISBN 0470091819. info
• JENSEN, Frank. Introduction to computational chemistry. 2nd ed. Chichester: John Wiley & Sons, 2007, xx, 599. ISBN 9780470011874. info
• REMKO, Milan. Molekulové modelovanie :princípy a aplikácie. Bratislava: Slovak Academic Press, 2000, 239 s. ISBN 80-88908-62-0. 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 can also be completed outside the examination period.
The course is taught annually.

C7800 Computational Chemistry and Molecular Modeling I seminar

Extent and Intensity

0/1/0. 1 credit(s). Type of Completion: z (credit).

Teacher(s)

RNDr. Petr Kulhánek, Ph.D. (lecturer)
Mgr. Tomáš Bouchal, Ph.D. (seminar tutor)
Mgr. Ivo Durník, Ph.D. (seminar tutor)

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 18:00–18:50 C04/118

Prerequisites

NOW( C7790 Computat. Chem. and Molec. I )
Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. Knowledge of UNIX operation system is advantage.

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: 2/30, 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

there are 13 fields of study the course is directly associated with, display

Course objectives

At the end of the course students should be able to understand and explain how to use one of the commonly used modeling software packages.

Learning outcomes

Student will be able to:
- create appropriate models of studied problems;
- perform basic quantum-chemical and molecular-mechanical calculations;
- calculate interaction energy;
- find the transition state of the elementary reaction and determine its activation energy;
- describe the dynamics of small molecular system;

Syllabus

• 1. Introduction to Gaussian program - http://www.gaussian.com/ (input data preparation, results analysis and their visualization - Molden, Molekel, VMD)
• 2. Introduction to Amber program package - http://ambermd.org/ (preparation of studied system, equilibration, dynamics, results analysis and their visualization - VMD)
• 3. Elaboration of independent projects

Literature

• LEACH, Andrew R. Molecular modelling : principles and applications. 2nd ed. Harlow: Prentice Hall, 2001, xxiii, 744. ISBN 0582382106. info
• CRAMER, Christopher J. Essentials of computational chemistry : theories and models. 2nd ed. Chichester: John Wiley & Sons, 2004, xx, 596. ISBN 0470091819. info
• JENSEN, Frank. Introduction to computational chemistry. 2nd ed. Chichester: John Wiley & Sons, 2007, xx, 599. ISBN 9780470011874. info
• REMKO, Milan. Molekulové modelovanie :princípy a aplikácie. Bratislava: Slovak Academic Press, 2000, 239 s. ISBN 80-88908-62-0. 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 can also be completed outside the examination period.
The course is taught annually.

C7800 Computational Chemistry and Molecular Modeling I seminar

Extent and Intensity

0/1/0. 1 credit(s). Type of Completion: z (credit).

Teacher(s)

RNDr. Petr Kulhánek, Ph.D. (lecturer)
Mgr. Tomáš Bouchal, Ph.D. (seminar tutor)
Mgr. Ivo Durník, Ph.D. (seminar tutor)

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 17:00–17:50 C04/118

Prerequisites

NOW( C7790 Computat. Chem. and Molec. I )
Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. Knowledge of UNIX operation system is advantage.

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

there are 13 fields of study the course is directly associated with, display

Course objectives

At the end of the course students should be able to understand and explain how to use one of the commonly used modeling software packages.

Learning outcomes

Student will be able to:
- create appropriate models of studied problems;
- perform basic quantum-chemical and molecular-mechanical calculations;
- calculate interaction energy;
- find the transition state of the elementary reaction and determine its activation energy;
- describe the dynamics of small molecular system;

Syllabus

• 1. Introduction to Gaussian program - http://www.gaussian.com/ (input data preparation, results analysis and their visualization - Molden, Molekel, VMD)
• 2. Introduction to Amber program package - http://ambermd.org/ (preparation of studied system, equilibration, dynamics, results analysis and their visualization - VMD)
• 3. Elaboration of independent projects

Literature

• LEACH, Andrew R. Molecular modelling : principles and applications. 2nd ed. Harlow: Prentice Hall, 2001, xxiii, 744. ISBN 0582382106. info
• CRAMER, Christopher J. Essentials of computational chemistry : theories and models. 2nd ed. Chichester: John Wiley & Sons, 2004, xx, 596. ISBN 0470091819. info
• JENSEN, Frank. Introduction to computational chemistry. 2nd ed. Chichester: John Wiley & Sons, 2007, xx, 599. ISBN 9780470011874. info
• REMKO, Milan. Molekulové modelovanie :princípy a aplikácie. Bratislava: Slovak Academic Press, 2000, 239 s. ISBN 80-88908-62-0. 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 can also be completed outside the examination period.
The course is taught annually.

C7800 Computational Chemistry and Molecular Modeling I seminar

Extent and Intensity

0/1/0. 1 credit(s). Type of Completion: z (credit).

Teacher(s)

RNDr. Petr Kulhánek, Ph.D. (lecturer)
prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Tomáš Bouchal, Ph.D. (seminar tutor)

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 17. 9. to Fri 14. 12. Mon 17:00–17:50 C04/118

Prerequisites

NOW( C7790 Computat. Chem. and Molec. I )
Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. Knowledge of UNIX operation system is advantage.

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

there are 13 fields of study the course is directly associated with, display

Course objectives

At the end of the course students should be able to understand and explain how to use one of the commonly used modeling software packages.

Syllabus

• 1. Introduction to Spartan program - http://www.wavefun.com/ (molecule building, calculation types, results analysis)
• 2. Introduction to Gaussian program - http://www.gaussian.com/ (input data preparation, results analysis and their visualization - Molden, Molekel, VMD)
• 3. Introduction to Amber program package - http://ambermd.org/ (preparation of studied system, equilibration, dynamics, results analysis and their visualization - VMD)
• 4. Elaboration of independent project

Literature

• LEACH, Andrew R. Molecular modelling : principles and applications. 2nd ed. Harlow: Prentice Hall, 2001, xxiii, 744. ISBN 0582382106. info
• CRAMER, Christopher J. Essentials of computational chemistry : theories and models. 2nd ed. Chichester: John Wiley & Sons, 2004, xx, 596. ISBN 0470091819. info
• JENSEN, Frank. Introduction to computational chemistry. 2nd ed. Chichester: John Wiley & Sons, 2007, xx, 599. ISBN 9780470011874. info
• REMKO, Milan. Molekulové modelovanie :princípy a aplikácie. Bratislava: Slovak Academic Press, 2000, 239 s. ISBN 80-88908-62-0. 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 can also be completed outside the examination period.
The course is taught annually.

C7800 Computational Chemistry and Molecular Modeling I seminar

Extent and Intensity

0/1/0. 1 credit(s). Type of Completion: z (credit).

Teacher(s)

RNDr. Petr Kulhánek, Ph.D. (lecturer)
prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Tomáš Bouchal, Ph.D. (seminar tutor)

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. 9. to Fri 15. 12. Mon 17:00–17:50 C04/118

Prerequisites

NOW( C7790 Computat. Chem. and Molec. I )
Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. Knowledge of UNIX operation system is advantage.

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

there are 13 fields of study the course is directly associated with, display

Course objectives

At the end of the course students should be able to understand and explain how to use one of the commonly used modeling software packages.

Syllabus

• 1. Introduction to Spartan program - http://www.wavefun.com/ (molecule building, calculation types, results analysis)
• 2. Introduction to Gaussian program - http://www.gaussian.com/ (input data preparation, results analysis and their visualization - Molden, Molekel, VMD)
• 3. Introduction to Amber program package - http://ambermd.org/ (preparation of studied system, equilibration, dynamics, results analysis and their visualization - VMD)
• 4. Elaboration of independent project

Literature

• LEACH, Andrew R. Molecular modelling : principles and applications. 2nd ed. Harlow: Prentice Hall, 2001, xxiii, 744. ISBN 0582382106. info
• CRAMER, Christopher J. Essentials of computational chemistry : theories and models. 2nd ed. Chichester: John Wiley & Sons, 2004, xx, 596. ISBN 0470091819. info
• JENSEN, Frank. Introduction to computational chemistry. 2nd ed. Chichester: John Wiley & Sons, 2007, xx, 599. ISBN 9780470011874. info
• REMKO, Milan. Molekulové modelovanie :princípy a aplikácie. Bratislava: Slovak Academic Press, 2000, 239 s. ISBN 80-88908-62-0. 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 can also be completed outside the examination period.
The course is taught annually.

C7800 Computational Chemistry and Molecular Modeling I seminar

Extent and Intensity

0/1/0. 1 credit(s). Type of Completion: z (credit).

Teacher(s)

RNDr. Petr Kulhánek, Ph.D. (lecturer)
prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Tomáš Bouchal, Ph.D. (seminar tutor)

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 19. 9. to Sun 18. 12. Mon 17:00–17:50 C04/118

Prerequisites

NOW( C7790 Computat. Chem. and Molec. I )
Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. Knowledge of UNIX operation system is advantage.

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

there are 13 fields of study the course is directly associated with, display

Course objectives

At the end of the course students should be able to understand and explain how to use one of the commonly used modeling software packages.

Syllabus

• 1. Introduction to Spartan program - http://www.wavefun.com/ (molecule building, calculation types, results analysis)
• 2. Introduction to Gaussian program - http://www.gaussian.com/ (input data preparation, results analysis and their visualization - Molden, Molekel, VMD)
• 3. Introduction to Amber program package - http://ambermd.org/ (preparation of studied system, equilibration, dynamics, results analysis and their visualization - VMD)
• 4. Elaboration of independent project

Literature

• LEACH, Andrew R. Molecular modelling : principles and applications. 2nd ed. Harlow: Prentice Hall, 2001, xxiii, 744. ISBN 0582382106. info
• CRAMER, Christopher J. Essentials of computational chemistry : theories and models. 2nd ed. Chichester: John Wiley & Sons, 2004, xx, 596. ISBN 0470091819. info
• JENSEN, Frank. Introduction to computational chemistry. 2nd ed. Chichester: John Wiley & Sons, 2007, xx, 599. ISBN 9780470011874. info
• REMKO, Milan. Molekulové modelovanie :princípy a aplikácie. Bratislava: Slovak Academic Press, 2000, 239 s. ISBN 80-88908-62-0. 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 can also be completed outside the examination period.
The course is taught annually.

C7800 Computational Chemistry and Molecular Modeling I seminar

Extent and Intensity

0/1/0. 1 credit(s). Type of Completion: z (credit).

Teacher(s)

RNDr. Petr Kulhánek, Ph.D. (lecturer)
prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Tomáš Bouchal, Ph.D. (seminar tutor)

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 17:00–17:50 C04/118

Prerequisites

NOW( C7790 Computat. Chem. and Molec. I )
Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. Knowledge of UNIX operation system is advantage.

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

there are 13 fields of study the course is directly associated with, display

Course objectives

At the end of the course students should be able to understand and explain how to use one of the commonly used modeling software packages.

Syllabus

• 1. Introduction to Spartan program - http://www.wavefun.com/ (molecule building, calculation types, results analysis)
• 2. Introduction to Gaussian program - http://www.gaussian.com/ (input data preparation, results analysis and their visualization - Molden, Molekel, VMD)
• 3. Introduction to Amber program package - http://ambermd.org/ (preparation of studied system, equilibration, dynamics, results analysis and their visualization - VMD)
• 4. Elaboration of independent project

Literature

• LEACH, Andrew R. Molecular modelling : principles and applications. 2nd ed. Harlow: Prentice Hall, 2001, xxiii, 744. ISBN 0582382106. info
• CRAMER, Christopher J. Essentials of computational chemistry : theories and models. 2nd ed. Chichester: John Wiley & Sons, 2004, xx, 596. ISBN 0470091819. info
• JENSEN, Frank. Introduction to computational chemistry. 2nd ed. Chichester: John Wiley & Sons, 2007, xx, 599. ISBN 9780470011874. info
• REMKO, Milan. Molekulové modelovanie :princípy a aplikácie. Bratislava: Slovak Academic Press, 2000, 239 s. ISBN 80-88908-62-0. 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 can also be completed outside the examination period.
The course is taught annually.

C7800 Computational Chemistry and Molecular Modeling I seminar

Extent and Intensity

0/1/0. 1 credit(s). Type of Completion: z (credit).

Teacher(s)

prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
RNDr. Petr Kulhánek, Ph.D. (lecturer)
Mgr. Jakub Štěpán, Ph.D. (seminar tutor)

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 17:00–17:50 C04/118

Prerequisites

NOW( C7790 Computat. Chem. and Molec. I )
Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. Knowledge of UNIX operation system is advantage.

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

there are 10 fields of study the course is directly associated with, display

Course objectives

At the end of the course students should be able to understand and explain how to use one of the commonly used modeling software packages.

Syllabus

• 1. Introduction to Spartan program - http://www.wavefun.com/ (molecule building, calculation types, results analysis)
• 2. Introduction to Gaussian program - http://www.gaussian.com/ (input data preparation, results analysis and their visualization - Molden, Molekel, VMD)
• 3. Introduction to Amber program package - http://ambermd.org/ (preparation of studied system, equilibration, dynamics, results analysis and their visualization - VMD)
• 4. Elaboration of independent project

Literature

• JENSEN, Frank. Introduction to computational chemistry. 2nd ed. Chichester: John Wiley & Sons, 2007, xx, 599. ISBN 9780470011874. info
• REMKO, Milan. Molekulové modelovanie :princípy a aplikácie. Bratislava: Slovak Academic Press, 2000, 239 s. ISBN 80-88908-62-0. info
• LIPKOWITZ, K B and D B BOYD. Reviews in Computational Chemistry 1-9. New York: VCH Publishers, 1998. 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 can also be completed outside the examination period.
The course is taught annually.

C7800 Computational Chemistry and Molecular Modeling I seminar

Extent and Intensity

0/1/0. 1 credit(s). Type of Completion: z (credit).

Teacher(s)

prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
RNDr. Petr Kulhánek, Ph.D. (lecturer)
Mgr. Jakub Štěpán, Ph.D. (seminar tutor)

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 17:00–17:50 C04/211

Prerequisites

NOW( C7790 Computat. Chem. and Molec. I )
Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. Knowledge of UNIX operation system is advantage.

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

there are 10 fields of study the course is directly associated with, display

Course objectives

At the end of the course students should be able to understand and explain how to use one of the commonly used modeling software packages.

Syllabus

• 1. Introduction to Spartan program - http://www.wavefun.com/ (molecule building, calculation types, results analysis)
• 2. Introduction to Gaussian program - http://www.gaussian.com/ (input data preparation, results analysis and their visualization - Molden, Molekel, VMD)
• 3. Introduction to Amber program package - http://ambermd.org/ (preparation of studied system, equilibration, dynamics, results analysis and their visualization - VMD)
• 4. Elaboration of independent project

Literature

• JENSEN, Frank. Introduction to computational chemistry. 2nd ed. Chichester: John Wiley & Sons, 2007, xx, 599. ISBN 9780470011874. info
• REMKO, Milan. Molekulové modelovanie :princípy a aplikácie. Bratislava: Slovak Academic Press, 2000, 239 s. ISBN 80-88908-62-0. info
• LIPKOWITZ, K B and D B BOYD. Reviews in Computational Chemistry 1-9. New York: VCH Publishers, 1998. 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 can also be completed outside the examination period.
The course is taught annually.

C7800 Computational Chemistry and Molecular Modeling I seminar

Extent and Intensity

0/1/0. 1 credit(s) (fasci plus compl plus > 4). Type of Completion: z (credit).

Teacher(s)

prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
RNDr. Petr Kulhánek, Ph.D. (lecturer)
Mgr. Jakub Štěpán, Ph.D. (seminar tutor)

Guaranteed by

prof. RNDr. Jaroslav Koča, DrSc.
National Centre for Biomolecular Research – Faculty of Science
Supplier department: National Centre for Biomolecular Research – Faculty of Science

Timetable

Mon 16:00–16:50 C04/118

Prerequisites

NOW( C7790 Computat. Chem. and Molec. I )
Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. Knowledge of UNIX operation system is advantage.

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 8 fields of study the course is directly associated with, display

Course objectives

At the end of the course students should be able to understand and explain how to use one of the commonly used modeling software packages.

Syllabus

• 1. Introduction to Spartan program - http://www.wavefun.com/ (molecule building, calculation types, results analysis)
• 2. Introduction to Gaussian program - http://www.gaussian.com/ (input data preparation, results analysis and their visualization - Molden, Molekel, VMD)
• 3. Introduction to Amber program package - http://ambermd.org/ (preparation of studied system, equilibration, dynamics, results analysis and their visualization - VMD)
• 4. Elaboration of independent project

Literature

• JENSEN, Frank. Introduction to computational chemistry. 2nd ed. Chichester: John Wiley & Sons, 2007, xx, 599. ISBN 9780470011874. info
• REMKO, Milan. Molekulové modelovanie :princípy a aplikácie. Bratislava: Slovak Academic Press, 2000, 239 s. ISBN 80-88908-62-0. info
• LIPKOWITZ, K B and D B BOYD. Reviews in Computational Chemistry 1-9. New York: VCH Publishers, 1998. 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 can also be completed outside the examination period.
The course is taught annually.

C7800 Computational Chemistry and Molecular Modeling I seminar

Extent and Intensity

0/1/0. 1 credit(s) (fasci plus compl plus > 4). Type of Completion: z (credit).

Teacher(s)

prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
RNDr. Petr Kulhánek, Ph.D. (lecturer)
Mgr. Jakub Štěpán, Ph.D. (seminar tutor)

Guaranteed by

prof. RNDr. Jaroslav Koča, DrSc.
National Centre for Biomolecular Research – Faculty of Science

Timetable

Mon 16:00–16:50 C04/211, Mon 16:00–16:50 C04/118

Prerequisites

NOW( C7790 Computat. Chem. and Molec. I )
Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. Knowledge of UNIX operation system is advantage.

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 9 fields of study the course is directly associated with, display

Course objectives

At the end of the course students should be able to understand and explain how to use one of the commonly used modeling software packages.

Syllabus

• 1. Introduction to Spartan program - http://www.wavefun.com/ (molecule building, calculation types, results analysis)
• 2. Introduction to Gaussian program - http://www.gaussian.com/ (input data preparation, results analysis and their visualization - Molden, Molekel, VMD)
• 3. Introduction to Amber program package - http://ambermd.org/ (preparation of studied system, equilibration, dynamics, results analysis and their visualization - VMD)
• 4. Elaboration of independent project

Literature

• JENSEN, Frank. Introduction to computational chemistry. 2nd ed. Chichester: John Wiley & Sons, 2007, xx, 599. ISBN 9780470011874. info
• REMKO, Milan. Molekulové modelovanie :princípy a aplikácie. Bratislava: Slovak Academic Press, 2000, 239 s. ISBN 80-88908-62-0. info
• LIPKOWITZ, K B and D B BOYD. Reviews in Computational Chemistry 1-9. New York: VCH Publishers, 1998. 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 can also be completed outside the examination period.
The course is taught annually.

C7800 Computational Chemistry and Molecular Modeling I seminar

Extent and Intensity

0/1/0. 1 credit(s) (fasci plus compl plus > 4). Type of Completion: z (credit).

Teacher(s)

prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
RNDr. Petr Kulhánek, Ph.D. (lecturer)

Guaranteed by

prof. RNDr. Jaroslav Koča, DrSc.
National Centre for Biomolecular Research – Faculty of Science

Timetable

Tue 18:00–18:50 C04/211

Prerequisites

NOW( C7790 Computat. Chem. and Molec. I )
Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. Knowledge of UNIX operation system is advantage.

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 9 fields of study the course is directly associated with, display

Course objectives

At the end of the course students should be able to understand and explain how to use one of the commonly used modeling software packages.

Syllabus

• 1. Introduction to Spartan program - http://www.wavefun.com/ (molecule building, calculation types, results analysis)
• 2. Introduction to Gaussian program - http://www.gaussian.com/ (input data preparation, results analysis and their visualization - Molden, Molekel, VMD)
• 3. Introduction to Amber program package - http://ambermd.org/ (preparation of studied system, equilibration, dynamics, results analysis and their visualization - VMD)
• 4. Elaboration of independent project

Literature

• JENSEN, Frank. Introduction to computational chemistry. 2nd ed. Chichester: John Wiley & Sons, 2007, xx, 599. ISBN 9780470011874. info
• REMKO, Milan. Molekulové modelovanie :princípy a aplikácie. Bratislava: Slovak Academic Press, 2000, 239 s. ISBN 80-88908-62-0. info
• LIPKOWITZ, K B and D B BOYD. Reviews in Computational Chemistry 1-9. New York: VCH Publishers, 1998. 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 can also be completed outside the examination period.
The course is taught annually.

C7800 Computational Chemistry and Molecular Modeling I seminar

Extent and Intensity

0/1/0. 1 credit(s) (fasci plus compl plus > 4). Type of Completion: z (credit).

Teacher(s)

prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Zdeněk Kříž, Ph.D. (lecturer)
RNDr. Petr Kulhánek, Ph.D. (lecturer)

Guaranteed by

prof. RNDr. Jaroslav Koča, DrSc.
National Centre for Biomolecular Research – Faculty of Science

Timetable

Thu 13:00–13:50 C04/211

Prerequisites

NOW( C7790 Computat. Chem. and Molec. I )
Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. Knowledge of UNIX operation system is advantage.

Course Enrolment Limitations

The course is only offered to the students of the study fields the course is directly associated with.

The capacity limit for the course is 10 student(s).
Current registration and enrolment status: enrolled: 0/10, only registered: 0/10

fields of study / plans the course is directly associated with

there are 9 fields of study the course is directly associated with, display

Course objectives

At the end of the course students should be able to understand and explain how to use one of the commonly used modeling software packages.

Syllabus

• 1. Introduction to Spartan program - http://www.wavefun.com/ (molecule building, calculation types, results analysis)
• 2. Introduction to Gaussian program - http://www.gaussian.com/ (input data preparation, results analysis and their visualization - Molden, Molekel, VMD)
• 3. Introduction to Amber program package - http://ambermd.org/ (preparation of studied system, equilibration, dynamics, results analysis and their visualization - VMD)
• 4. Elaboration of independent project

Literature

• JENSEN, Frank. Introduction to computational chemistry. 2nd ed. Chichester: John Wiley & Sons, 2007, xx, 599. ISBN 9780470011874. info
• REMKO, Milan. Molekulové modelovanie :princípy a aplikácie. Bratislava: Slovak Academic Press, 2000, 239 s. ISBN 80-88908-62-0. info
• LIPKOWITZ, K B and D B BOYD. Reviews in Computational Chemistry 1-9. New York: VCH Publishers, 1998. 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 can also be completed outside the examination period.
The course is taught annually.

C7800 Computational Chemistry and Molecular Modeling I seminar

Extent and Intensity

0/1/0. 1 credit(s) (fasci plus compl plus > 4). Type of Completion: z (credit).

Teacher(s)

prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Zdeněk Kříž, Ph.D. (lecturer)
RNDr. Petr Kulhánek, Ph.D. (lecturer)

Guaranteed by

prof. RNDr. Jaroslav Koča, DrSc.
National Centre for Biomolecular Research – Faculty of Science

Timetable

Mon 12:00–12:50 C04/211

Prerequisites

NOW( C7790 Computat. Chem. and Molec. I )
See C7790

Course Enrolment Limitations

The course is only offered to the students of the study fields the course is directly associated with.

The capacity limit for the course is 10 student(s).
Current registration and enrolment status: enrolled: 0/10, only registered: 0/10

fields of study / plans the course is directly associated with

there are 9 fields of study the course is directly associated with, display

Course objectives

See C7790

Syllabus

• See C7790

Literature

• JENSEN, Frank. Introduction to computational chemistry. 2nd ed. Chichester: John Wiley & Sons, 2007, xx, 599. ISBN 9780470011874. info
• REMKO, Milan. Molekulové modelovanie :princípy a aplikácie. Bratislava: Slovak Academic Press, 2000, 239 s. ISBN 80-88908-62-0. info
• LIPKOWITZ, K B and D B BOYD. Reviews in Computational Chemistry 1-9. New York: VCH Publishers, 1998. info

Assessment methods

Individual project.

Language of instruction

Czech

Further comments (probably available only in Czech)

Study Materials
The course can also be completed outside the examination period.
The course is taught annually.

C7800 Computational Chemistry and Molecular Modeling I seminar

Extent and Intensity

0/1/0. 1 credit(s) (fasci plus compl plus > 4). Type of Completion: z (credit).

Teacher(s)

prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Zdeněk Kříž, Ph.D. (lecturer)

Guaranteed by

prof. RNDr. Jaroslav Koča, DrSc.
National Centre for Biomolecular Research – Faculty of Science

Timetable

Wed 11:00–11:50 C04/211

Prerequisites

NOW( C7790 Computat. Chem. and Molec. I )
See C7790

Course Enrolment Limitations

The course is only offered to the students of the study fields the course is directly associated with.

The capacity limit for the course is 10 student(s).
Current registration and enrolment status: enrolled: 0/10, only registered: 0/10

fields of study / plans the course is directly associated with

there are 13 fields of study the course is directly associated with, display

Course objectives

See C7790

Syllabus

• See C7790

Assessment methods (in Czech)

Jde o cvičení typu samostatného projektu. Studenti si volí téma buď podle svého odborného zaměření (například konformační analýza látek se kterými pracují, studium reakčního mechanismu apod.) nebo podle zadání vyučujícího. Zápočet je udělen za dokončení projektu a jeho obhájení.

Language of instruction

Czech

Further comments (probably available only in Czech)

The course can also be completed outside the examination period.
The course is taught annually.

C7800 Computational Chemistry and Molecular Modeling I seminar

Extent and Intensity

0/1/0. 1 credit(s) (fasci plus compl plus > 4). Type of Completion: z (credit).

Teacher(s)

prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Zdeněk Kříž, Ph.D. (lecturer)

Guaranteed by

prof. RNDr. Jaroslav Koča, DrSc.
National Centre for Biomolecular Research – Faculty of Science

Timetable

Mon 10:00–10:50 C04/211

Prerequisites

NOW( C7790 Computat. Chem. and Molec. I )
See C7790

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 12 fields of study the course is directly associated with, display

Course objectives

See C7790

Syllabus

• See C7790

Assessment methods (in Czech)

Jde o cvičení typu samostatného projektu. Studenti si volí téma buď podle svého odborného zaměření (například konformační analýza látek se kterými pracují, studium reakčního mechanismu apod.) nebo podle zadání vyučujícího. Zápočet je udělen za dokončení projektu a jeho obhájení.

Language of instruction

Czech

Further comments (probably available only in Czech)

The course can also be completed outside the examination period.
The course is taught annually.

C7800 Computational Chemistry and Molecular Modeling I seminar

Extent and Intensity

0/1/0. 1 credit(s) (fasci plus compl plus > 4). Type of Completion: z (credit).

Teacher(s)

prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Zdeněk Kříž, Ph.D. (lecturer)

Guaranteed by

prof. RNDr. Jaroslav Koča, DrSc.
Chemistry Section – Faculty of Science

Timetable

Mon 16:00–16:50 C04/211

Prerequisites

NOW( C7790 Computat. Chem. and Molec. I )
See C7790

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 12 fields of study the course is directly associated with, display

Course objectives

See C7790

Syllabus

• See C7790

Assessment methods (in Czech)

Jde o cvičení typu samostatného projektu. Studenti si volí téma buď podle svého odborného zaměření (například konformační analýza látek se kterými pracují, studium reakčního mechanismu apod.) nebo podle zadání vyučujícího. Zápočet je udělen za dokončení projektu a jeho obhájení.

Language of instruction

Czech

Further comments (probably available only in Czech)

The course can also be completed outside the examination period.
The course is taught annually.

C7800 Computational Chemistry and Molecular Modeling I seminar

Extent and Intensity

0/0/1. 1 credit(s) (fasci plus compl plus > 4). Type of Completion: z (credit).

Teacher(s)

prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Zdeněk Kříž, Ph.D. (lecturer)

Guaranteed by

prof. RNDr. Jaroslav Koča, DrSc.
Chemistry Section – Faculty of Science

Prerequisites

NOW( C7790 Computat. Chem. and Molec. I )
See C7790

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 10 student(s).
Current registration and enrolment status: enrolled: 0/10, only registered: 0/10, only registered with preference (fields directly associated with the programme): 0/10

fields of study / plans the course is directly associated with

there are 12 fields of study the course is directly associated with, display

Course objectives

See C7790

Syllabus

• See C7790

Assessment methods (in Czech)

Jde o cvičení typu samostatného projektu. Studenti si volí téma buď podle svého odborného zaměření (například konformační analýza látek se kterými pracují, studium reakčního mechanismu apod.) nebo podle zadání vyučujícího. Zápočet je udělen za dokončení projektu a jeho obhájení.

Language of instruction

Czech

Further comments (probably available only in Czech)

Information on completion of the course: Projekt
The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every week.

C7800 Computational Chemistry and Molecular Modeling I seminar

Extent and Intensity

0/1/0. 1 credit(s) (fasci plus compl plus > 4). Type of Completion: z (credit).

Teacher(s)

prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Zdeněk Kříž, Ph.D. (lecturer)

Guaranteed by

prof. RNDr. Jaroslav Koča, DrSc.
Chemistry Section – Faculty of Science

Prerequisites

NOW( C7790 Computat. Chem. and Molec. I )
See C7790

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 12 fields of study the course is directly associated with, display

Course objectives

See C7790

Syllabus

• See C7790

Assessment methods (in Czech)

Jde o cvičení typu samostatného projektu. Studenti si volí téma buď podle svého odborného zaměření (například konformační analýza látek se kterými pracují, studium reakčního mechanismu apod.) nebo podle zadání vyučujícího. Zápočet je udělen za dokončení projektu a jeho obhájení.

Language of instruction

Czech

Further comments (probably available only in Czech)

The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every week.

C7800 Computational Chemistry and Molecular Modeling I seminar

Extent and Intensity

0/1/0. 1 credit(s) (fasci plus compl plus > 4). Type of Completion: z (credit).

Teacher(s)

prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Zdeněk Kříž, Ph.D. (lecturer)

Guaranteed by

prof. RNDr. Jaroslav Koča, DrSc.
Chemistry Section – Faculty of Science

Prerequisites

NOW( C7790 Computat. Chem. and Molec. I )
See C7790

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 12 fields of study the course is directly associated with, display

Course objectives

See C7790

Syllabus

• See C7790

Assessment methods (in Czech)

Jde o cvičení typu samostatného projektu. Studenti si volí téma buď podle svého odborného zaměření (například konformační analýza látek se kterými pracují, studium reakčního mechanismu apod.) nebo podle zadání vyučujícího. Zápočet je udělen za dokončení projektu a jeho obhájení.

Language of instruction

Czech

Further comments (probably available only in Czech)

The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every week.

C7800 Computational Chemistry and Molecular Modeling I

Extent and Intensity

0/1/0. 1 credit(s). Type of Completion: z (credit).

Teacher(s)

prof. RNDr. Jaroslav Koča, DrSc. (lecturer)

Guaranteed by

prof. RNDr. Jaroslav Koča, DrSc.
Chemistry Section – Faculty of Science

Prerequisites (in Czech)

NOW( C7790 Computat. Chem. and Molec. )

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 12 fields of study the course is directly associated with, display

Language of instruction

Czech

Further Comments

The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every week.

C7800 Computational Chemistry and Molecular Modeling I

Extent and Intensity

0/1/0. 1 credit(s). Type of Completion: z (credit).

Teacher(s)

prof. RNDr. Jaroslav Koča, DrSc. (lecturer)

Guaranteed by

prof. RNDr. Jaroslav Koča, DrSc.
Chemistry Section – Faculty of Science

Prerequisites (in Czech)

NOW( C7790 Computat. Chem. and Molec. )

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 12 fields of study the course is directly associated with, display

Language of instruction

Czech

Further Comments

The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every week.

C7800 Computational Chemistry and Molecular Modeling I seminar

The information about the term Autumn 2011 - acreditation is not made public

Extent and Intensity

0/1/0. 1 credit(s) (fasci plus compl plus > 4). Type of Completion: z (credit).

Teacher(s)

prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
RNDr. Petr Kulhánek, Ph.D. (lecturer)

Guaranteed by

prof. RNDr. Jaroslav Koča, DrSc.
National Centre for Biomolecular Research – Faculty of Science

Prerequisites

NOW( C7790 Computat. Chem. and Molec. I )
Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. Knowledge of UNIX operation system is advantage.

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 9 fields of study the course is directly associated with, display

Course objectives

At the end of the course students should be able to understand and explain how to use one of the commonly used modeling software packages.

Syllabus

• 1. Introduction to Spartan program - http://www.wavefun.com/ (molecule building, calculation types, results analysis)
• 2. Introduction to Gaussian program - http://www.gaussian.com/ (input data preparation, results analysis and their visualization - Molden, Molekel, VMD)
• 3. Introduction to Amber program package - http://ambermd.org/ (preparation of studied system, equilibration, dynamics, results analysis and their visualization - VMD)
• 4. Elaboration of independent project

Literature

• JENSEN, Frank. Introduction to computational chemistry. 2nd ed. Chichester: John Wiley & Sons, 2007, xx, 599. ISBN 9780470011874. info
• REMKO, Milan. Molekulové modelovanie :princípy a aplikácie. Bratislava: Slovak Academic Press, 2000, 239 s. ISBN 80-88908-62-0. info
• LIPKOWITZ, K B and D B BOYD. Reviews in Computational Chemistry 1-9. New York: VCH Publishers, 1998. 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 can also be completed outside the examination period.
The course is taught annually.
The course is taught: every week.

C7800 Computational Chemistry and Molecular Modeling I seminar

Extent and Intensity

0/1/0. 1 credit(s) (fasci plus compl plus > 4). Type of Completion: z (credit).

Teacher(s)

prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
RNDr. Petr Kulhánek, Ph.D. (lecturer)

Guaranteed by

prof. RNDr. Jaroslav Koča, DrSc.
National Centre for Biomolecular Research – Faculty of Science

Prerequisites

NOW( C7790 Computat. Chem. and Molec. I )
Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. Knowledge of UNIX operation system is advantage.

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 9 fields of study the course is directly associated with, display

Course objectives

At the end of the course students should be able to understand and explain how to use one of the commonly used modeling software packages.

Syllabus

• 1. Introduction to Spartan program - http://www.wavefun.com/ (molecule building, calculation types, results analysis)
• 2. Introduction to Gaussian program - http://www.gaussian.com/ (input data preparation, results analysis and their visualization - Molden, Molekel, VMD)
• 3. Introduction to Amber program package - http://ambermd.org/ (preparation of studied system, equilibration, dynamics, results analysis and their visualization - VMD)
• 4. Elaboration of independent project

Literature

• JENSEN, Frank. Introduction to computational chemistry. 2nd ed. Chichester: John Wiley & Sons, 2007, xx, 599. ISBN 9780470011874. info
• REMKO, Milan. Molekulové modelovanie :princípy a aplikácie. Bratislava: Slovak Academic Press, 2000, 239 s. ISBN 80-88908-62-0. info
• LIPKOWITZ, K B and D B BOYD. Reviews in Computational Chemistry 1-9. New York: VCH Publishers, 1998. 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 can also be completed outside the examination period.
The course is taught annually.
The course is taught: every week.

C7800 Computational Chemistry and Molecular Modeling I seminar

Extent and Intensity

0/1/0. 1 credit(s) (fasci plus compl plus > 4). Type of Completion: z (credit).

Teacher(s)

prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Zdeněk Kříž, Ph.D. (lecturer)

Guaranteed by

prof. RNDr. Jaroslav Koča, DrSc.
National Centre for Biomolecular Research – Faculty of Science

Prerequisites

NOW( C7790 Computat. Chem. and Molec. I )
See C7790

Course Enrolment Limitations

The course is only offered to the students of the study fields the course is directly associated with.

fields of study / plans the course is directly associated with

there are 17 fields of study the course is directly associated with, display

Course objectives

See C7790

Syllabus

• See C7790

Assessment methods (in Czech)

Jde o cvičení typu samostatného projektu. Studenti si volí téma buď podle svého odborného zaměření (například konformační analýza látek se kterými pracují, studium reakčního mechanismu apod.) nebo podle zadání vyučujícího. Zápočet je udělen za dokončení projektu a jeho obhájení.

Language of instruction

Czech

Further comments (probably available only in Czech)

The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every week.

• Enrolment Statistics (recent)