Difference between revisions of "Advanced Simulation Methods SS 2018"
m (→Worksheet) 

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==== Literature ====  ==== Literature ====  
−  :* C. Holm.<br />'''"Simulating Long range interactions".'''<br />''Institute for Computational Physics, Universitat Stuttgart,'' '''2018'''.<br />  +  :* C. Holm.<br />'''"Simulating Long range interactions".'''<br />''Institute for Computational Physics, Universitat Stuttgart,'' '''2018'''. <br /> [[Media:longrange.pdf[PDF]]] (15.4 MB) <br /> 
<bibentry>deserno98a,arnold13b,arnold05a</bibentry>  <bibentry>deserno98a,arnold13b,arnold05a</bibentry>  
−  === Part 2:  +  === Part 2: ElectroOsmotic Flow === 
==== Description ====  ==== Description ====  
[[File:Slitpore.png550pxrightElectroosmotic flow in a slit pore]]  [[File:Slitpore.png550pxrightElectroosmotic flow in a slit pore]]  
Line 213:  Line 213:  
in the figure to the right. In this exercise you should simulate such a system with [http://espressomd.org ESPResSo].  in the figure to the right. In this exercise you should simulate such a system with [http://espressomd.org ESPResSo].  
You are supposed to use a Lattice Boltzmann fluid coupled to explicit ions which are represented  You are supposed to use a Lattice Boltzmann fluid coupled to explicit ions which are represented  
−  by charge WeekChandlerAnderson spheres. In addition to the charge on the walls, the ions are also subject to an external  +  by charge WeekChandlerAnderson spheres. 
−  electrical field parallel to the walls. Electrostatics should be handled by the P3M algorithm.  +  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 with ELC.  
A set of realistic parameters and an more in detail description of the system can be found in the  A set of realistic parameters and an more in detail description of the system can be found in the  
thesis.  thesis.  
You should measure the flow profile of the fluid and the density and velocity profiles of the ions. The case of the slit  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  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 (DebyeHueckelLimit). Calculate the ion profiles in one or both of these cases and compare the results with  +  salt limit (DebyeHueckelLimit). 
−  the simulation.  +  Calculate the ion profiles in one or both of these cases and compare the results with the simulation. 
−  ====  +  ===== Worksheet ===== 
−  General part and parts 4 & 6 of [  +  
+  {{Downloadadv_sm_mod3_EOF.pdfDetailed worksheet}}  
+  
+  ==== Literature ====  
+  
+  Some ESPResSo tutorials can be helpful.  
+  * General part and parts 4 & 6 of [https://github.com/espressomd/espresso/blob/python/doc/tutorials/04lattice_boltzmann/04lattice_boltzmann.pdf the LatticeBoltzmann tutorial]  
+  * Part 7 of the [https://github.com/espressomd/espresso/blob/python/doc/tutorials/02charged_system/02charged_system.pdf charged systems tutorial] to see how to setup proper electrostatics in quasi2D geometry.  
−  Georg Rempfer, {{DownloadBSc_thesis_rempfer.pdf"LatticeBoltzmann Simulations in Complex Geometries"}}, 2010, Institute for Computational Physics, Stuttgart  +  * Georg Rempfer, {{DownloadBSc_thesis_rempfer.pdf"LatticeBoltzmann Simulations in Complex Geometries"}}, 2010, Institute for Computational Physics, Stuttgart 
−  
=== Part 3: Electrophoresis of Polyelectrolytes ===  === Part 3: Electrophoresis of Polyelectrolytes ===  
==== Description ====  ==== Description ====  
In this part you simulate the movement of a charged polymer under the influence of an external electrical field and hydrodynamic interactions.  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  +  Set up a system consisting of a charged polymer, ions with the opposite charge to make the system neutral and an Lattice Boltzmann fluid coupled with 
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  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  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).  experimental results (see literature).  
−  ==== Instructions and  +  
+  ==== Worksheet ====  
+  {{Downloadadv_sm_mod3_elpho.pdfDetailed worksheet}}  
+  
+  ==== Instructions and Literature ====  
General part and part 5 of [[Media:04lattice_boltzmann.pdf]]  General part and part 5 of [[Media:04lattice_boltzmann.pdf]]  
Latest revision as of 12:11, 9 July 2018
A preliminary registration for this course is mandatory. Interested students should send an email to Maria Fyta as soon as possible.
First meeting: Friday, April 13 at 11:30 in the ICP meeting room (Allmandring 3, 1st floor, room 1.095).
Overview
 Type
 Lecture and Tutorials (2 SWS in total)
 Lecturer
 Prof. Dr. Christian Holm, JP. Dr. Maria Fyta, Dr. Frank Uhlig, Dr. David Sean
 Course language
 English or German
 Location
 ICP, Allmandring 3; Room: ICP Meeting Room
 Time
 (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 TBA. Module 1: Maria Fyta, Frank Uhlig, Interatomic interactions modeled with quantum mechanical simulations
Dates
First meeting: Friday, April 13 at 11:30 in the ICP meeting room (Allmandring 3, 1st floor, room 1.095).
Tutorials: TBA in the ICP CIPPool.
Talks: TBA am in the ICP meeting room.
Description
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 DFTrelated 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. MoriSanchez, and W. Yang, Chemical Reviews 112, 289 (2012); dx.doi.org/10.1021/cr200107z.
Contact
If you have any questions regarding the organization or content of this module please do not hesitate to contact Maria Fyta. For practical guidance regarding the simulations Frank Uhlig.
Density functional theory and exchangecorrelation functionals
Description
Many modern catalyses are performed using noble metals. In particular at the surface of these catalysts, which come in a multitude of shapes and chemical composition. The overall catalysis is determined by many factors, including the actual reactivity of chemical species at the surface, adsorption of reactants and desorption of products, as well as kinetics of the diffusion on the surface.
In this exercise you will look at the desorption behavior of hydrogen gas from the surface of noble metals. This process is important in the production of hydrogen gas for energy storage applications [1]. However, modeling this process using modern methods of quantummechanical density functional theory (DFT) is very challenging. Only very advanced and quite recent density functionals are able to describe the longrange dispersion interactions [2]. Hence, effective methods based on pair potentials have been developed. These methods can achieve comparable accuracy to more ab initio methods while coming at a signifcantly lower computational effort [3,4].
Your task is to develop such a pairwise dispersion correction for the interaction of hydrogen gas with a metal surface. The first step is to understand and document the metallic behavior of your metal substrate, followed by investigation of the performance of common DFT functionals for the desorption process, and finally developing a dispersion correction by determining individual dispersion coefficients for the involved species [5].
[1] https://dx.doi.org/10.1038/ncomms6848
[2] https://dx.doi.org/10.1063/1.4754130
[3] https://dx.doi.org/10.1103/PhysRevLett.102.073005
[4] https://dx.doi.org/10.1063/1.3382344
[5] https://dx.doi.org/10.1063/1.2746031
Literature
 A bird'seye view of densityfunctional theory, Klaus Capelle, arXiv:condmat/0211443 (2002).
 SelfConsistent 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, MinCheol 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 densityfunctional theory exchangecorrelation 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 Hbonded 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).
Report
Please write a report 510 pages containing and discussing your results and hand it in by Friday TBA.
Module 2: Maria Fyta, Narayanan Krishnamoorthy Anand: Atomistic Simulations of CoSolutes in Aqueous Solutions
Dates
First meeting: 18.05.2018 in the ICP meeting room.
Final meeting: 15.06.2018 in the ICP meeting room.
Deadline for reports: 15.06.2018
Description
This module focuses on atomistic Molecular Dynamics simulations and the study of biological cosolutes like urea, ectoine or hydroxyectoine and their influence on aqueous solutions. Biological cosolutes, often also called osmolytes are omnipresent in biological cells. A main function of these smallweight 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.
Contact
If you have any questions regarding the organization or content of this module, please do not hesitate to contact Narayanan Krishnamoorthy Anand.
Part 1: Osmolytes and KirkwoodBuff Theory
Description
This part introduces the students to the field of osmolyte research. An important theory to study solvation and binding behavior is given by the KirkwoodBuff 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 KirkwoodBuff theory in the context of the simulations.
Literature
 D. R. Canchi and A. E. Garcia, "Cosolvent 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)
 S. Weerasinghe and P. E. Smith, "A Kirkwood–Buff derived force field for sodium chloride in water", The Journal of Chemical Physics 119, 11342 (2003).
 J. Rösgen, B. M. Pettitt and D. W. Bolen, "Protein folding, stability, and solvation structure in osmolyte solutions", Biophys. J. 89, 2988 (2005)
 J. Smiatek, "Osmolyte effects: Impact on the aqueous solution around charged and neutral spheres", J. Phys. Chem. B 118, 771 (2014)
 T. Kobayashi et al, "The properties of residual water molecules in ionic liquids: a comparison between direct and inverse Kirkwood–Buff approaches", Phys.Chem.Chem.Phys. 19, 18924 (2017)
Part 2: Model Development and Simulations
Description
This part is practical. The simulations will be conducted by the software package GROMACS [1]. The students will develop Generalized Amber Force Fields (GAFF) [2] with the help of the ACPYPE program [3] 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 KirkwoodBuff 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
 itpFile for Hydroxyectoine (7 KB)
 groFile for Hydroxyectoine (682 bytes)
 itpFile for Ectoine (6 KB)
 groFile 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 2030 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 waterwater, waterosmolyte and osmolyteosmolyte 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 waterwater, waterosmolyte and osmolyteosmolyte pairs. Use this information to compute the
 KirkwoodBuff 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).
Literature
 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)
Report
Please write a report of about 5 pages containing and discussing your results and hand it in until TBA.
Module 3: Christian Holm, Electrostatics, Lattice Boltzmann, and Electrokinetics
Dates
First meeting: TBA in the ICP meeting room.
Final meeting: TBA in the ICP meeting room.
Description
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:
Contact
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
Description
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.
Literature
 C. Holm.
"Simulating Long range interactions".
Institute for Computational Physics, Universitat Stuttgart, 2018.
[PDF] (15.4 MB)
 C. Holm.

Deserno, Markus and Holm, Christian.
"How to mesh up Ewald sums. I. A theoretical and numerical comparison of various particle mesh routines".
The Journal of Chemical Physics 109(7678), 1998.
[PDF] (307 KB) [DOI] 
Arnold, Axel and Fahrenberger, Florian and Holm, Christian and Lenz, Olaf and Bolten, Matthias and Dachsel, Holger and Halver, Rene and Kabadshow, Ivo and Gähler, Franz and Heber, Frederik and Iseringhausen, Julian and Hofmann, Michael and Pippig, Michael and Potts, Daniel and Sutmann, Godehard.
"Comparison of scalable fast methods for longrange interactions".
Physical Review E 88(063308), 2013.
[PDF] (3 MB) [DOI] 
Axel Arnold and Christian Holm.
"Efficient methods to compute long range interactions for soft matter systems".
In Advanced Computer Simulation Approaches for Soft Matter Sciences II, volume of Advances in Polymer Science, pages 59–109. Editors: C. Holm and K. Kremer,
Springer, Berlin, 2005.
[PDF] (2 MB) [DOI]
Part 2: ElectroOsmotic Flow
Description
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 WeekChandlerAnderson 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 with ELC. 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 (DebyeHueckelLimit). Calculate the ion profiles in one or both of these cases and compare the results with the simulation.
Worksheet
Detailed worksheet (92 KB)
Literature
Some ESPResSo tutorials can be helpful.
 General part and parts 4 & 6 of the LatticeBoltzmann tutorial
 Part 7 of the charged systems tutorial to see how to setup proper electrostatics in quasi2D geometry.
 Georg Rempfer, "LatticeBoltzmann Simulations in Complex Geometries" (1.36 MB), 2010, Institute for Computational Physics, Stuttgart
Part 3: Electrophoresis of Polyelectrolytes
Description
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 charged polymer, ions with the opposite charge to make the system neutral and an Lattice Boltzmann fluid coupled with 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).
Worksheet
Detailed worksheet (93 KB)
Instructions and Literature
General part and part 5 of Media:04lattice_boltzmann.pdf

Kai Grass and Ute Böhme and Ulrich Scheler and Hervé Cottet and Christian Holm.
"Importance of Hydrodynamic Shielding for the Dynamic Behavior of Short Polyelectrolyte Chains".
Physical Review Letters 100(096104), 2008.
[PDF] (115 KB) [DOI] 
Grass, Kai Christian.
"Towards realistic modelling of free solution electrophoresis: a case study on charged macromolecules".
PhD thesis, GoetheUniversität Frankfurt am Main, 2008.
[PDF] (6 MB)
Report
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, TBA