1. Quantum ESPRESSO-Grid
Kanchan Sonkar (
Centre of Biomedical Magnetic Resonance
SGPGIMS-Campus, Lucknow, India
Asia Joint CHAIN/EU-IndiaGrid2/EPIKH Workshop
Kolkata,

2. Outline Structure elucidation using Quantum ESPRESSO
Proteins
Nuclear Magnetic Resonance spectroscopy
Quantum ESPRESSO
Running QE on Grid
Results of the run
Future aspects
Summary and conclusion
References
Kolkata, EPIKH Workshop,

3. Structure elucidation
Proteins
Most important biological molecule
Perform various functions
Tissue regeneration
Immune responses for human body
Cellular signalling and molecular transport
Specialized protein classes for various processes
Most abundant proteins
Involve in almost all cellular processes
Kolkata, EPIKH Workshop,

4. Peripheral membrane proteins Integral membrane proteins
Type
Peripheral membrane proteins
Integral membrane proteins
Glycoprotein
Spectrin
Accessory
Kolkata, EPIKH Workshop,

5. Peptide chains held together by hydrogen bonds between peptide bonds of adjacent peptide chains
The N-H of every peptide bond is hydrogen- bonded to the carbonyl group of the peptide bond 4 amino acids away
Kolkata, EPIKH Workshop,

6. Structure elucidation techniques
X-ray crystallography
Protein must be in crystallized form
Atomic force method
Provides only surface information
Solution NMR
Unsuitable for membrane proteins
Solid state NMR
Most promising techniques
Kolkata, EPIKH Workshop,

7. Nuclear Magnetic Resonance (NMR) spectroscopy
Relies on magnetic properties of nuclei, which behave like tiny bar magnets Bo
Kolkata, EPIKH Workshop,

8. Resonance frequency is directly proportional to
Gyromagnetic ratio
Applied magnetic field
At B=11.7 T (tesla, 104 Gauss) the resonant frequency for 1H is 500 MHz
Kolkata, EPIKH Workshop,

9. Other useful nuclei used in NMR
Frequency (MHz) at
sensitivity (relative)
sensitivity (absolute)
Isotope
Spin I
Abundance(%)
1H /
2H x x x
13C / x x
14N x x
15N / x x
19F /
23Na 3/ x x
31P / x x
113Cd 1/ x x
Kolkata, EPIKH Workshop,

10. NMR spectrometer
Kolkata, EPIKH Workshop,

11. Spin in a magnetic field B0 Magnetization lies along z-axis
rf pulse application on z-magnetization
Relaxation of magnetization
Kolkata, EPIKH Workshop,

12. Signal recorded in the form of Free Induction Decay (FID)
FID (time domain signal)
Spectrum (frequency domain signal)
Kolkata, EPIKH Workshop,

13. Interpretation of NMR spectrum
Chemical shift
Defines local environment of nuclei
Nuclei resonate at different Larmor frequencies
Larmor frequency depends upon
Local environment
Presence of other magnetic nuclei
Shielding tensor
Chemical shift
Chemical shift can be calculated as
Some reference compounds:
● 1H, 13C, 29Si → tetramethylsilane (TMS)
● 15N → liquid NH3
● 17O → liquid H2O
● 19F → liquid CFCl3
● 27Al → AlCl3 in D2O
● 43Ca → CaCl2(aq) 1 mol/L
Kolkata, EPIKH Workshop,

14. Chemical shift range 1H
13C
Kolkata, EPIKH Workshop,

15. Solid State NMR Molecules in liquids move very fast In solids
Giving sharp NMR lines (isotropic chemical shift)
In solids
No movement is possible
Hence, broad NMR peaks (anisotropy)
No averaging of spin interaction-broader lines
Poly crystalline line shape
Kolkata, EPIKH Workshop,

16. Averaging of spin interactions Some interactions depend on
Magic angle spinning
Effect of Magic Angle Spinning on Glycine
Kolkata, EPIKH Workshop,

17. Kolkata, EPIKH Workshop, 18.02.2011

18. NMR parameters for structure elucidation
Chemical shift
Kolkata, EPIKH Workshop,

19. Quantum ESPRESSO
Kolkata, EPIKH Workshop,

20. Stands for opEn Source Package for Research in Electronic Structure, Simulation, and Optimization
Integrated suite of codes for electronic structure calculation
Freely available to researchers
Simulations/computations include
calculation of the Kohn–Sham (KS) orbitals and energies
complete structural optimizations of the microscopic (atomic coordinates) and macroscopic (unit cell) degrees of freedom
ab initio molecular dynamics (MD)
Calculation of second and third derivatives of total energy at any wavelength
Calculation of nuclear magnetic resonance (NMR) and electronic paramagnetic resonance (EPR) parameters
Kolkata, EPIKH Workshop,

21. Running QE on Grid
pw.x to calculate the total energy and the band structure of four simple systems: Si, Al, Cu, Ni .
JDL file used
Calculation [
JobType = "Normal“;
Executable = "run-qe.sh";
#Arguments = "";
StdOutput = "qe.out";
StdError = "qe.err";
InputSandbox = {"run-qe.sh","espresso.tgz","ompi tgz","lcg-rec-cp","lcg-rec-cr"};
OutputSandbox = {"qe.err","qe.out"}; ]
make a self-consistent calculation for each molecule
Calculates the Band structure for each molecule
Kolkata, EPIKH Workshop,

22. Results of the run Results al.band.cg.out al.band.david.out
al.scf.cg.out
al.scf.david.out
si.band.cg.out
si.band.david.out
si.scf.cg.out
si.scf.david.out
cu.band.cg.out
cu.band.david.out
cu.scf.cg.out
cu.scf.david.out
ni.band.cg.out
ni.band.david.out
ni.scf.cg.out
ni.scf.david.out
Kolkata, EPIKH Workshop,

23. Future aspects Running parallel job on Grid
Computing carbon-alpha and carbonyl-carbon chemical shift parameters
Kolkata, EPIKH Workshop,

24. Summary & Conclusions
Study will be useful for understanding performance of Quantum ESPRESSO on Grid
Final outcome of study will be helpful for determining the structure of larger sized proteins
Will help in advancement of Computational NMR
Kolkata, EPIKH Workshop,

25. References
QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials, Paolo Giannozzi, Stefano Baroni, Nicola Bonini, Matteo Calandra, Roberto Car, Carlo Cavazzoni, Davide Ceresoli, Guido L Chiarotti, Matteo Cococcioni, Ismaila Dabo, Andrea Dal Corso, Stefano de Gironcoli, Stefano Fabris, Guido Fratesi, Ralph Gebauer, Uwe Gerstmann, Christos Gougoussis, Anton Kokalj, Michele Lazzeri, Layla Martin-Samos, Nicola Marzari, Francesco Mauri, Riccardo Mazzarello, Stefano Paolini, Alfredo Pasquarello, Lorenzo Paulatto, Carlo Sbraccia, Sandro Scandolo, Gabriele Sclauzero, Ari P Seitsonen, Alexander Smogunov, Paolo Umari and Renata M Wentzcovitch , J. Phys.: Condens. Matter 21, (2009).
All-electron magnetic response with pseudopotentials: NMR chemical shifts, Chris j, Pickard and Francesco Mauri: Phys. Rev. B 63,245101(2001)
Kolkata, EPIKH Workshop,

26. Training school Training School
Useful in understanding the Grid infrastructure and
porting applications on Grid
Importing and exporting our input and output data
Helpful understanding the concepts of grid, starting from applying for certification and its management
Theory and practical sessions were interactive and very informative
Mentors were very helpful
Wonderful experience
Kolkata, EPIKH Workshop,

27. Thank you
Kolkata, EPIKH Workshop,

28. Questions …