Difference between revisions of "Advanced Simulation Methods SS 2019"

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<b> Files </b>{{Download|AdvSimMethoMod1.zip| AdvSimMethoMod1.zip}}
 
<b> Files </b>{{Download|AdvSimMethoMod1.zip| AdvSimMethoMod1.zip}}
  
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Pseudopotential for LMKLL-VDW {{Download|C_VDW.psf| C_VDW.psf}} (rename it to C.psf in order to use it in SIESTA)
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[[Media:Graphene.png]]
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[[Media:Graphene_layers.png]]
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[[Media:Graphite.png]]
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[[Media:Graphite_layers.png]]
  
 
==== Literature ====
 
==== Literature ====
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<b> Lecture Notes </b>{{Download|advSimMeth_module1_XCfunct.pdf| Module 1}}
 
<b> Lecture Notes </b>{{Download|advSimMeth_module1_XCfunct.pdf| Module 1}}
  
== Module 2: [[Maria Fyta]], [[]]: Atomistic Simulations of Co-Solutes in Aqueous Solutions ==
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== Module 2: [[Maria Fyta]], [[Takeshi Kobayashi]]: Atomistic Simulations of Co-Solutes in Aqueous Solutions ==
  
  
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=== Contact ===
 
=== Contact ===
  
If you have any questions regarding the organization or content of this module, please do not hesitate to contact [[Narayanan Krishnamoorthy Anand]].
+
If you have any questions regarding the organization or content of this module, please do not hesitate to contact [[Takeshi Kobayashi]].
  
 
=== Part 1: Osmolytes and Kirkwood-Buff Theory ===
 
=== Part 1: Osmolytes and Kirkwood-Buff Theory ===
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* T. Kobayashi <i>et al</i>, "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)
 
* T. Kobayashi <i>et al</i>, "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 ===
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=== Part 2: Simulations ===
  
 
==== Description ====
 
==== Description ====
  
This part is practical. The simulations will be conducted by the software package GROMACS [http://www.gromacs.org/]. The students will develop Generalized Amber Force Fields (GAFF) [http://ambermd.org/antechamber/gaff.html] with the help of the ACPYPE program [http://www.ccpn.ac.uk/v2-software/software/ACPYPE-folder] 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).
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This part is practical. The simulations will be conducted by the software package GROMACS [http://www.gromacs.org/]. The students will perform the simulations of ionic liquids(IL)-water mixtures at different water concentration in combination with the SPC/E water model and OPLSAA force field for EMImBF4. To generate the initial configuration of the simulation boxes, the software package Packmol [http://www.ime.unicamp.br/~martinez/packmol] will be used.
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 ====
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First the students simulate pure water and pure IL, and analyze the output data. Following properties will be calculated. The Kirkwood-Buff theory will be used to calculate the Kirkwood-Buff integrals. The student perform the different simulation box size to estimate the proper box size for calculating the properties.
 +
* Kirkwood-Buff integrals
 +
* diffusion coefficients
 +
* mass densities
 +
In addition to above, for water
 +
* hydrogen bond life times and number of hydrogen bonds for water-water pairs
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* water mean relaxation times
 +
 
 +
Next the student perform the IL-water mixtures at different water concentrations. After energy minimization and warm up, run 500 ns simulations with GROMACS for water mole fractions between X_H2O = 0 - 0.30.
 +
 +
In comparison to pure water/pure IL, the students will analyze several properties stated above and elucidate their water concentration dependent behavior.
 +
Interpret the corresponding results with regard to the findings in Phys.Chem.Chem.Phys. 19, 18924 (2017). 
 +
 
 +
All the data needed for the exercise can be found in /group/sm/2019/Advsm_part2
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 +
<!--
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==== Force Fields for IL(EMImBF4) ====
  
 
* {{Download| hectoinzwittmp2.itp |itp-File for Hydroxyectoine}}
 
* {{Download| hectoinzwittmp2.itp |itp-File for Hydroxyectoine}}
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* {{Download| ectoinzwittmp2.itp |itp-File for Ectoine}}
 
* {{Download| ectoinzwittmp2.itp |itp-File for Ectoine}}
 
* {{Download| ectoinzwittmp2.gro |gro-File for Ectoine}}
 
* {{Download| ectoinzwittmp2.gro |gro-File for Ectoine}}
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-->
  
=== Part 3: Tasks ===
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<!--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.
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:
 
2. Study the following properties for the different osmolytes and concentrations:
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3. Calculate the radial distribution functions for all systems in terms of water-water, water-osmolyte and osmolyte-osmolyte pairs.
 
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
 
Use this information to compute the
* Kirkwood-Buff integrals
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* derivatives of the chemical activity
 
* derivatives of the chemical activity
 
* derivatives of the activity coefficient
 
* derivatives of the activity coefficient
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* 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)
 
* 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)
 
* 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)
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-->
  
 
== Module 3: [[Christian Holm]], [[Rudolph Weeber]] Electrostatics, Lattice Boltzmann, and Electrokinetics==
 
== Module 3: [[Christian Holm]], [[Rudolph Weeber]] Electrostatics, Lattice Boltzmann, and Electrokinetics==
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=== Contact ===
 
=== Contact ===
 
If you have any questions regarding the organisation or content of this module please do not hesitate to contact [[Christian Holm]].
 
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]].
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For questions regarding the practical part of the module and technical help contact [[Rudolf Weeber]].
  
 
=== Part 1: Electrostatics ===
 
=== Part 1: Electrostatics ===
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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).
 
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
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The final report is due electronically July 17, TBA
  
  
  
 
<!--Please write together one report of 5 to 10 pages containing and discussing your simulation results from part 2 and 3.-->
 
<!--Please write together one report of 5 to 10 pages containing and discussing your simulation results from part 2 and 3.-->

Latest revision as of 22:36, 20 June 2019

Overview

Type
Lecture and Tutorials (2 SWS in total)
Lecturer
Prof. Dr. Christian Holm, JP. Dr. Maria Fyta
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 and JP. Dr. Maria Fyta. It 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 of about 10 pages on each module, which they should submit to the responsible person for each module by the deadline set for each module.


Module 1: Maria Fyta, Frank Maier, Inter-atomic interactions modeled with quantum mechanical simulations

Dates

First meeting: Friday, April 12 at 11:30 in the ICP meeting room (Allmandring 3, 1st floor, room 1.095).

Final meeting and presentation: Friday, May 10 at 11:30 in the ICP meeting room (Allmandring 3, 1st floor, room 1.095).

Tutorials: Fridays 11:30-13:00 in the ICP CIP-Pool. The first tutorial will take place on Wed. April 17 at 15:00-16:30.

Deadline for reports: Mai 08, 2019

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 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.

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 exchange-correlation functionals

Description

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 the tutorial.

Overall, a variety of DFT exchange correlation functionals have been developed. Some of these often fail in describe complex interactions. For example, only very advanced and quite recent density functionals are able to describe the long-range 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 [2,3].

[1] https://dx.doi.org/10.1063/1.4754130

[2] https://dx.doi.org/10.1103/PhysRevLett.102.073005

[3] https://dx.doi.org/10.1063/1.3382344

Tutorial

In this exercise you will test different exchange correlation functionals for two systems (silicon and graphite) and analyze the results. All simulations will be performed with the software package SIESTA. A thorough analysis of the stability and energetics of the two system is expected. Tutorial files and brief instructions can be found in ?. The software is installed on our CIP pool machines under /group/allatom/.

Files application_zip.png AdvSimMethoMod1.zip (11.89 MB)Info circle.png


Pseudopotential for LMKLL-VDW text_plain.png C_VDW.psf (140 KB)Info circle.png (rename it to C.psf in order to use it in SIESTA)

Media:Graphene.png

Media:Graphene_layers.png

Media:Graphite.png

Media:Graphite_layers.png

Literature

  • 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).
  • 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).
  • Electronic properties of nano-graphene sheets calculated using quantum chemical DFT
  • Sangam Banerjeea, , Dhananjay Bhattacharyya, Computational Materials Science, 44, 41–45 (2008).
  • 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).

Further reading (if interested)

  • 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).

Lecture Notes application_pdf.png Module 1 (2.22 MB)Info circle.png

Module 2: Maria Fyta, Takeshi Kobayashi: Atomistic Simulations of Co-Solutes in Aqueous Solutions

Dates

First meeting: Friday May 10 at 13:00 in the ICP meeting room.

Final meeting and presentation: Friday, June 07 at 11:30 in the ICP meeting room (Allmandring 3, 1st floor, room 1.095).

Tutorials: Fridays 11:30-13:00 in the ICP CIP-Pool.

Deadline for reports: June 05, 2019

Description

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.

Contact

If you have any questions regarding the organization or content of this module, please do not hesitate to contact Takeshi Kobayashi.

Part 1: Osmolytes and Kirkwood-Buff 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 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.

Literature

  • 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)
  • 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: Simulations

Description

This part is practical. The simulations will be conducted by the software package GROMACS [1]. The students will perform the simulations of ionic liquids(IL)-water mixtures at different water concentration in combination with the SPC/E water model and OPLSAA force field for EMImBF4. To generate the initial configuration of the simulation boxes, the software package Packmol [2] will be used.

First the students simulate pure water and pure IL, and analyze the output data. Following properties will be calculated. The Kirkwood-Buff theory will be used to calculate the Kirkwood-Buff integrals. The student perform the different simulation box size to estimate the proper box size for calculating the properties.

  • Kirkwood-Buff integrals
  • diffusion coefficients
  • mass densities

In addition to above, for water

  • hydrogen bond life times and number of hydrogen bonds for water-water pairs
  • water mean relaxation times

Next the student perform the IL-water mixtures at different water concentrations. After energy minimization and warm up, run 500 ns simulations with GROMACS for water mole fractions between X_H2O = 0 - 0.30.

In comparison to pure water/pure IL, the students will analyze several properties stated above and elucidate their water concentration dependent behavior. Interpret the corresponding results with regard to the findings in Phys.Chem.Chem.Phys. 19, 18924 (2017).

All the data needed for the exercise can be found in /group/sm/2019/Advsm_part2


Module 3: Christian Holm, Rudolph Weeber Electrostatics, Lattice Boltzmann, and Electrokinetics

Dates

First meeting: June 21 at 11:30 in the ICP meeting room.

Final meeting and presentation: Friday, July 19 at 11:30 in the ICP meeting room (Allmandring 3, 1st floor, room 1.095).

Tutorials: Fridays 11:30-13:00 in the ICP CIP-Pool.

Deadline for reports: July 17, 2019

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 Rudolf Weeber.

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)


Part 2: Electro-Osmotic Flow

Description

Electroosmotic flow in a 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 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 (Debye-Hueckel-Limit). Calculate the ion profiles in one or both of these cases and compare the results with the simulation.

Worksheet

application_pdf.pngDetailed worksheet (92 KB)Info circle.png

Literature

Some ESPResSo tutorials can be helpful.

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

application_pdf.pngDetailed worksheet (93 KB)Info circle.png

Instructions and Literature

General part and part 5 of Media:04-lattice_boltzmann.pdf


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 July 17, TBA