Advanced Simulation Methods SS 2017
A preliminary registration for this course is mandatory. Interested students should send an email to Maria Fyta as soon as possible.
- 1 Overview
- 2 Module 1: Maria Fyta, Frank Uhlig, Inter-atomic interactions modeled with quantum mechanical simulations
- 3 Module 2: Jens Smiatek, Julian Michalowsky: Atomistic Simulations of Co-Solutes in Aqueous Solutions
- 4 Module 3: Christian Holm, Electrostatics, Lattice Boltzmann, and Electrokinetics
- Lecture and Tutorials (2 SWS in total)
- Prof. Dr. Christian Holm, Dr. Jens Smiatek, JP. Dr. Maria Fyta
- Course language
- English or German
- ICP, Allmandring 3; Room: ICP Meeting Room
- (see below)
The course will consist of three modules supervised by Prof. Dr. Christian Holm, Dr. Jens Smiatek, JP. Dr. Maria Fyta and will contain exercises, presentations, discussion meetings, and written reports, worked out in groups. Each group will have to give a talk for all modules. The students can work in groups. All groups should write a report on each module, which they should submit to the responsible person for each module by the deadline set for each module.
A preliminary registration for this course is mandatory. Interested students write an Email to Maria Fyta until 01.04.2017.
Module 1: Maria Fyta, Frank Uhlig, Inter-atomic interactions modeled with quantum mechanical simulations
First meeting: 26.04.2017 at 13:00 in the ICP seminar room.
Tutorials: TBA in the ICP CIP-Pool.
Talks: 04.05.2017 at 09:30 am in the ICP meeting room.
This module focuses on the influence of using quantum mechanical simulations. The quantum mechanical schemes which will be applied in this module are based on density functional theory (DFT). This method allows the investigation of the electronic properties of a system. An understanding of the method, an analysis of the results from the simulations is the main goal of this module. The analysis of the simulations should be written up in a report. The talk will be a presentation of a DFT-related journal paper. For this, one of the following papers can be chosen:
- Perspective: Advances and challenges in treating van der Waals dispersion forces in density functional theory, J. Klimeš and A. Michaelides, The Journal of Chemical Physics 137, 120901 (2012); doi: 10.1063/1.4754130
- Challenges for Density Functional Theory, A.J. Cohen, P. Mori-Sanchez, and W. Yang, Chemical Reviews 112, 289 (2012); dx.doi.org/10.1021/cr200107z.
Part 1: Density functional theory and exchange-correlation functionals
This part introduces the students to the density functional theory (DFT) method. A scheme which has revolutionarized the way materials and their properties are studied. The students should focus on this method and understand how it works and which its capabilities are. A specific focus would be the different levels of approximations that can be made in this method. For this, the choice of the exchange-correlation functional mapping the interactions of a system is crucial. To this end, the discussion in this module will be directed. The report should contain an introduction to the exchange-correlation functionals in DFT in the context of the simulations and the analysis of the simulations in Part 2.
- A bird's-eye view of density-functional theory, Klaus Capelle, arXiv:cond-mat/0211443 (2002).
- Self-Consistent Equations Including Exchange and Correlation Effects, W. Kohn and L.J. Sham, , Phys. Rev. (140), A1133 (1965).
- Understanding and Reducing Errors in Density Functional Calculations, Min-Cheol Kim, Eunji Sim, and Kieron Burke, Phys. Rev. Lett. 111, 073003 (2013).
- An application of the van der Waals density functional: Hydrogen bonding and stacking interactions between nucleobases, V.R. Cooper, T. Thonhauser, and D.C. Langreth, J. Chem. Phys. 128, 204102 (2008).
- On the accuracy of density-functional theory exchange-correlation functionals for H bonds in small water clusters: Benchmarks approaching the complete basis set limit, B. Santra, A. Michaelides, and M. Scheffler, J. Chem. Phys. 127, 184104 (2007).
- On geometries of stacked and H-bonded nucleic acid base pairs determined at various DFT, MP2, and CCSD(T) levels up to the CCSD(T)/complete basis set limit level, I. Dąbkowska, P. Jurečka, and P. Hobza, J. Chem. Phys. 122, 204322 (2005).
Part 2: Stability and energetics of graphene layers and H30 radicals
This part is practical and involves the simulation of two different systems: (a) two stacked graphene planes and (b) a H3O radical. All simulations will be performed with the software package GPAW. The students should test the use of different exchange-correlation functionals. A thorough analysis of the stability and energetics of the two system is expected. Tutorial files and brief instructions can be found online at AdvancedSM. The software is installed on our CIP pool machines under /group/allatom/asmsoft/build.
- Impact of the electron-electron correlation on phonon dispersion: Failure of LDA and GGA DFT functionals in graphene and graphite, Michele Lazzeri, Claudio Attaccalite, Ludger Wirtz, and Francesco Mauri, Phys. Rev. B 78, 081406(R) (2008).
- From a localized H3O radical to a delocalized H3O+⋯e− solvent-separated pair by sequential hydration, Frank Uhlig, Ondrej Marsalek, and Pavel Jungwirth, Phys. Chem. Chem. Phys., 2011,13, 14003-14009
- Electronic properties of nano-graphene sheets calculated using quantum chemical DFT
- Sangam Banerjeea, , Dhananjay Bhattacharyya, Computational Materials Science, 44, 41–45 (2008).
- Benchmark calculations of water–acene interaction energies: Extrapolation to the water–graphene limit and assessment of dispersion–corrected DFT methods, Glen R. Jenness , Ozan Karalti and Kenneth D. Jordan, Phys. Chem. Chem. Phys., 12, 6375-6381 (2010).
- Dependence of band structures on stacking and field in layered graphene, Masato Aoki, , Hiroshi Amawashi, Solid State Communications 142, 123–127 (2007).
- Graphite Interplanar Bonding: Electronic Delocalization and van der Waals Interaction, J.-C. Charlier, X. Gonze and J.-P. Michenaud, Europhysics Letters), 28 , 403 (1994).
Please write a report 5-10 pages containing and discussing your results and hand it in by Friday 26.05.2017.
Module 2: Jens Smiatek, Julian Michalowsky: Atomistic Simulations of Co-Solutes in Aqueous Solutions
First meeting: June 1st, 2017 at 14:30 in the ICP meeting room.
Final meeting: July 6th, 2017 at 13:30 in the ICP meeting room.
Deadline for reports: June 29th, 2017
This module focuses on atomistic Molecular Dynamics simulations and the study of biological co-solutes like urea, ectoine or hydroxyectoine and their influence on aqueous solutions. Biological co-solutes, often also called osmolytes are omnipresent in biological cells. A main function of these small-weight organic molecules is given by the protection of protein structures under harsh environmental conditions (protein stabilizers) or the denaturation of proteins (protein denaturants). The underlying mechanism leading to these effects is still unknown. It has been often discussed that osmolytes have a significant impact on the aqueous solution. The module consists of model development, simulation, analysis and oral and written presentation part.
If you have any questions regarding the organization or content of this module, please do not hesitate to contact Jens Smiatek.
Part 1: Osmolytes and Kirkwood-Buff Theory
This part introduces the students to the field of osmolyte research. An important theory to study solvation and binding behavior is given by the Kirkwood-Buff theory which can be well applied to computer simulations. The students should study the literature given below and present their findings. The presentation should at a minimum contain an introduction to Kirkwood-Buff theory in the context of the simulations.
- D. R. Canchi and A. E. Garcia, "Co-solvent effects on protein stability", Ann. Rev. Phys. Chem. 64. 273 (2013)
- J. G. Kirkwood and F. P. Buff. "The statistical mechanical theory of solutions. I." J. Chem. Phys. 19, 774 (1951)
- V. Pierce, M. Kang, M. Aburi, S. Weerasinghe and P. E. Smith, "Recent applications of Kirkwood–Buff theory to biological systems", Cell Biochem. Biophys. 50, 1 (2008)
- J. Rösgen, B. M. Pettitt and D. W. Bolen, "Uncovering the basis for nonideal behavior of biological molecules", Biochemistry 43, 14472 (2004)
- J. Rösgen, B. M. Pettitt and D. W. Bolen, "Protein folding, stability, and solvation structure in osmolyte solutions", Biophys. J. 89, 2988 (2005)
- P. E. Smith, "Chemical potential derivatives and preferential interaction parameters in biological systems from Kirkwood-Buff Theory", Biophys. J. 91, 849 (2006)
- J. Smiatek, "Aqueous ionic liquids and their effects on protein structures: an overview on recent theoretical and experimental results", J. Phys. Condens. Matt. 29, 233001 (2017)
- J. Smiatek, "Osmolyte effects: Impact on the aqueous solution around charged and neutral spheres", J. Phys. Chem. B 118, 771 (2014)
Part 2: Model Development and Simulations
This part is practical. The simulations will be conducted by the software package GROMACS . The students will develop Generalized Amber Force Fields (GAFF)  with the help of the ACPYPE program  for the osmolytes (urea, hydroxyectoine, ectoine) which will be used for the study of solvent properties like the thermodynamics of hydrogen bonding ans the diffusivity according to J. Phys. Chem. B 118, 771 (2014). In comparison to pure water, the students will analyze several water parameters and elucidate the differences in presence of osmolytes and their concentration dependent behavior. The Kirkwood-Buff theory will be used to calculate derivatives of the activity coefficients and the derivative of the chemical activity for the osmolytes.
Force Fields for ectoine and hydroxyectoine
- itp-File for Hydroxyectoine (7 KB)
- gro-File for Hydroxyectoine (682 bytes)
- itp-File for Ectoine (6 KB)
- gro-File for Ectoine (592 bytes)
Part 3: Tasks
1. Implement the developed force fields for the osmolytes (urea, ectoine and hydroxyectoine) in combination with the SPC/E water model. After energy minimization and warm up, run 20-30 ns simulations with GROMACS for osmolyte concentrations between c = 0 - 6 M.
2. Study the following properties for the different osmolytes and concentrations:
- diffusion coefficients
- hydrogen bond life times and number of hydrogen bonds for water-water, water-osmolyte and osmolyte-osmolyte pairs
- water mean relaxation times
Interpret the corresponding results. Are the molecules kosmotropes or chaotropes?
3. Calculate the radial distribution functions for all systems in terms of water-water, water-osmolyte and osmolyte-osmolyte pairs. Use this information to compute the
- Kirkwood-Buff integrals
- derivatives of the chemical activity
- derivatives of the activity coefficient
Interpret the corresponding results with regard to the findings in Biochemistry 43, 14472 (2004).
- D. van der Spoel, P. J. van Maaren, P. Larsson and N. Timneanu, "Thermodynamics of hydrogen bonding in hydrophilic and hydrophobic media", J. Phys. Chem. B 110, 4393 (2006)
- J. Wang, R. M. Wolf, J. W. Caldwell, P. A. Kollman and D. A. Case, "Development and testing of a general amber force field", J. Comp. Chem. 25, 1157 (2004)
Please write a report of about 5 pages containing and discussing your results and hand it in until 'July 6th, 2017.
Module 3: Christian Holm, Electrostatics, Lattice Boltzmann, and Electrokinetics
First meeting: TBA in the ICP meeting room.
Final meeting: TBA in the ICP meeting room.
This module focuses on charged matter with electrostatic and hydrodynamic interactions. It should be taken in groups of three people. It consists of one lecture on electrostatic algorithms, simulations, theory, a presentation and a short report on the simulation results. You only have to give one common presentation and hand in one report. The Module 3 consists of three parts:
If you have any questions regarding the organisation or content of this module please do not hesitate to contact Christian Holm. For questions regarding the practical part of the module and technical help contact David Sean.
Part 1: Electrostatics
This part is about the theory of electrostatic algorithms for molecular dynamics simulations. It is concerned with state of the art algorithms beyond the Ewald sum, especially mesh Ewald methods. To this end the students should read the referenced literature. Christian Holm will give an hour long lecture. Afterwards we will discuss the content and try to resolve open questions. The presentation should foster the students understanding of the P3M method as well as give them an overview of its performance compared to other modern electrostatics methods.
- A. Arnold.
"Coulomb interactions: P3M, MMMxD, ELC and ICC∗".
Institute for Computational Physics, Universitat Stuttgart, 2012.
[PDF] (1.41 MB)
- A. Arnold.
Part 2: Slit Pore
This part is practical. It is concerned with the movement of ions in an charged slit pore. It is similar to the systems that are discussed in the Bachelors thesis of Georg Rempfer which is recommended reading. A slit pore consists of two infinite charge walls as shown in the figure to the right. In this exercise you should simulate such a system with ESPResSo. You are supposed to use a Lattice Boltzmann fluid coupled to explicit ions which are represented by charge Week-Chandler-Anderson spheres. In addition to the charge on the walls, the ions are also subject to an external electrical field parallel to the walls. Electrostatics should be handled by the P3M algorithm. A set of realistic parameters and an more in detail description of the system can be found in the thesis. You should measure the flow profile of the fluid and the density and velocity profiles of the ions. The case of the slit pore can be solved analytically either in the case of only counter ions (the so called salt free case) or in the high salt limit (Debye-Hueckel-Limit). Calculate the ion profiles in one or both of these cases and compare the results with the simulation.
Instructions and Literature
General part and parts 4 & 6 of Media:04-lattice_boltzmann.pdf
Georg Rempfer, "Lattice-Boltzmann Simulations in Complex Geometries" (1.36 MB), 2010, Institute for Computational Physics, Stuttgart
Part 3: Electrophoresis of Polyelectrolytes
In this part you simulate the movement of a charged polymer under the influence of an external electrical field and hydrodynamic interactions. Set up a system consisting of a charge polymer, ions with the opposite charge to make the system neutral and an Lattice Boltzmann fluid coupled the the ions and polymer. Apply an external field and measure the center of mass velocity of the polymer as a function of the length of the polymer for polymers of one to 20 monomers. Make sure the system is in equilibrium before you start the sampling. Compare your result to theory and experimental results (see literature).
Instructions and Literatur
General part and part 5 of Media:04-lattice_boltzmann.pdf
At the final meeting day of this module, one group will give a presentation about the learned and performed work. In addition, they write a report of about 5 pages containing and discussing the obtained results and hand it in together with the reports of the other modules at the end of the course (see above).
The final report is due electronically Friday night, 22.07.2016, 24:00