Quantum ESPRESSO-Grid Kanchan Sonkar ( kanchi2209@gmail.com) Centre of Biomedical Magnetic Resonance SGPGIMS-Campus, Lucknow, India Asia 2 2011-Joint CHAIN/EU-IndiaGrid2/EPIKH Workshop Kolkata, 18.02.2011

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, 18.02.2011

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, 18.02.2011

Peripheral membrane proteins Integral membrane proteins Type Peripheral membrane proteins Integral membrane proteins Glycoprotein Spectrin Accessory Kolkata, EPIKH Workshop, 18.02.2011

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, 18.02.2011

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, 18.02.2011

Nuclear Magnetic Resonance (NMR) spectroscopy Relies on magnetic properties of nuclei, which behave like tiny bar magnets Bo Kolkata, EPIKH Workshop, 18.02.2011

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, 18.02.2011

Other useful nuclei used in NMR Frequency (MHz) at 2.3488 sensitivity (relative) sensitivity (absolute) Isotope Spin I Abundance(%) 1H 1/2 99.98 1.00 1.00 100.000 2H 1 1.5x10-2 9.65x10-3 1.45x10-6 15.351 13C 1/2 1.108 1.59x10-2 1.76x10-4 25.144 14N 1 99.63 1.01x10-3 1.01x10-3 7.224 15N 1/2 0.37 1.04x10-3 3.85x10-6 10.133 19F 1/2 100 0.83 0.83 94.077 23Na 3/2 100 9.25x10-2 9.25x10-2 26.451 31P 1/2 100 6.63x10-2 6.63x10-2 40.481 113Cd 1/2 12.26 1.09x10-2 1.33x10-3 22.182 Kolkata, EPIKH Workshop, 18.02.2011

NMR spectrometer Kolkata, EPIKH Workshop, 18.02.2011

Spin in a magnetic field B0 Magnetization lies along z-axis rf pulse application on z-magnetization Relaxation of magnetization Kolkata, EPIKH Workshop, 18.02.2011

Signal recorded in the form of Free Induction Decay (FID) FID (time domain signal) Spectrum (frequency domain signal) Kolkata, EPIKH Workshop, 18.02.2011

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, 18.02.2011

Chemical shift range 1H 13C Kolkata, EPIKH Workshop, 18.02.2011

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, 18.02.2011

Averaging of spin interactions Some interactions depend on Magic angle spinning Effect of Magic Angle Spinning on Glycine Kolkata, EPIKH Workshop, 18.02.2011

Kolkata, EPIKH Workshop, 18.02.2011

NMR parameters for structure elucidation Chemical shift Kolkata, EPIKH Workshop, 18.02.2011

Quantum ESPRESSO Kolkata, EPIKH Workshop, 18.02.2011

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, 18.02.2011

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-1.4.3.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, 18.02.2011

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, 18.02.2011

Future aspects Running parallel job on Grid Computing carbon-alpha and carbonyl-carbon chemical shift parameters Kolkata, EPIKH Workshop, 18.02.2011

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, 18.02.2011

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, 395502 (2009). All-electron magnetic response with pseudopotentials: NMR chemical shifts, Chris j, Pickard and Francesco Mauri: Phys. Rev. B 63,245101(2001) http://www.quantum-espresso.org http://media.quantum-espresso.org/ Kolkata, EPIKH Workshop, 18.02.2011

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, 18.02.2011

Thank you Kolkata, EPIKH Workshop, 18.02.2011

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