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Intro to Molecular Dynamics (MD) Simulation using CHARMM

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Presentation on theme: "Intro to Molecular Dynamics (MD) Simulation using CHARMM"β€” Presentation transcript:

1 Intro to Molecular Dynamics (MD) Simulation using CHARMM
DaVID CHATFIELD, FIU DEPARTMENT OF CHEMISTRY AND BIOCHEMISTRY Workshop on Macromolecular Modeling FIU, April 8-9, 2017

2 Overview Principles of MD MD Program Structure System Preparation
Running MD Analyzing Results

3 A. Force Fields Quantum mechanics (QM): too expensive for macromolecules Force fields: method of choice Constructed from experimental data and QM calculations on small molecules Principle of transferability οƒ  atom type

4 Bonded and Non-bonded Terms
𝑉= 𝐸 π‘π‘œπ‘›π‘‘π‘’π‘‘ + 𝐸 π‘›π‘œπ‘›βˆ’π‘π‘œπ‘›π‘‘π‘’π‘‘

5 𝐸 π‘π‘œπ‘›π‘‘π‘’π‘‘ 𝐸 π‘π‘œπ‘›π‘‘π‘’π‘‘ = 𝐸 π‘π‘œπ‘›π‘‘βˆ’π‘ π‘‘π‘Ÿπ‘’π‘‘π‘β„Ž + 𝐸 π‘Žπ‘›π‘”π‘™π‘’βˆ’π‘π‘’π‘›π‘‘ + 𝐸 π‘‘π‘–β„Žπ‘’π‘‘π‘Ÿπ‘Žπ‘™ + … 𝐸 π‘π‘œπ‘›π‘‘βˆ’π‘ π‘‘π‘Ÿπ‘’π‘‘π‘β„Ž = π‘π‘œπ‘›π‘‘π‘  𝐾 𝑏 π‘βˆ’ 𝑏 0 2 𝐸 π‘Žπ‘›π‘”π‘™π‘’βˆ’π‘π‘’π‘›π‘‘ = π‘Žπ‘›π‘”π‘™π‘’π‘  𝐾 πœƒ πœƒβˆ’ πœƒ 0 2 𝐸 π‘‘π‘–β„Žπ‘’π‘‘π‘Ÿπ‘Žπ‘™ = π‘‘π‘–β„Žπ‘’π‘‘π‘Ÿπ‘Žπ‘™π‘  𝐾 πœ‘ 1+cos⁑ π‘›πœ‘βˆ’π›Ώ 2 A picture is worth a thousand words

6 𝐸 π‘π‘œπ‘›π‘‘π‘’π‘‘ Occasionally a few extra terms are included, e.g.
𝐸 π‘–π‘šπ‘π‘Ÿπ‘œπ‘π‘’π‘Ÿπ‘  (to maintain chirality & optimize fit to experiment) 𝐸 π‘ˆπ‘Ÿπ‘’π‘¦βˆ’π΅π‘Ÿπ‘Žπ‘‘π‘™π‘’π‘¦ (to optimize ..) CMAP (numerical correction and optimize ..) 𝐸 π‘–π‘šπ‘π‘Ÿπ‘œπ‘π‘’π‘Ÿπ‘  = π‘–π‘šπ‘π‘Ÿπ‘œπ‘π‘’π‘Ÿπ‘  𝐾 πœ” πœ”βˆ’ πœ” 0 2 𝐸 π‘ˆπ‘Ÿπ‘’π‘¦βˆ’π΅π‘Ÿπ‘Žπ‘‘π‘™π‘’π‘¦ = π‘ˆπ‘Ÿπ‘’π‘¦βˆ’π΅π‘Ÿπ‘Žπ‘‘π‘™π‘’π‘¦ 𝐾 π‘ˆπ΅ π‘†βˆ’π‘† 2 𝐸 𝐢𝑀𝐴𝑃 = π‘Ÿπ‘’π‘ π‘–π‘‘π‘’π‘’π‘  π‘ˆ 𝐢𝑀𝐴𝑃 πœ‘,πœ“

7 𝐸 π‘›π‘œπ‘›βˆ’π‘π‘œπ‘›π‘‘π‘’π‘‘ 𝐸 π‘›π‘œπ‘›βˆ’π‘π‘œπ‘›π‘‘π‘’π‘‘ = 𝐸 π‘£π‘Žπ‘› π‘‘π‘’π‘Ÿ π‘Šπ‘Žπ‘Žπ‘™π‘  + 𝐸 π‘’π‘™π‘’π‘π‘‘π‘Ÿπ‘œπ‘ π‘‘π‘Žπ‘‘π‘–π‘ 𝐸 π‘£π‘‘π‘Š= π‘›π‘œπ‘›βˆ’π‘π‘œπ‘›π‘‘π‘’π‘‘ π‘Žπ‘‘π‘œπ‘š π‘π‘Žπ‘–π‘Ÿπ‘  πœ€ 𝑖𝑗 π‘šπ‘–π‘› π‘Ÿ 𝑖𝑗 π‘šπ‘–π‘› π‘Ÿ 𝑖𝑗 12 βˆ’2 π‘Ÿ 𝑖𝑗 π‘šπ‘–π‘› π‘Ÿ 𝑖𝑗 6 𝐸 π‘’π‘™π‘’π‘π‘‘π‘Ÿπ‘œπ‘ π‘‘π‘Žπ‘‘π‘–π‘= π‘›π‘œπ‘›βˆ’π‘π‘œπ‘›π‘‘π‘’π‘‘ π‘Žπ‘‘π‘œπ‘š π‘π‘Žπ‘–π‘Ÿπ‘  π‘ž 𝑖 π‘ž 𝑗 4πœ‹ πœ€ π‘œ πœ€ π‘Ÿ 𝑖𝑗 rmin emin

8 Cut-offs Reduce computational demands
Makes 𝐸 π‘›π‘œπ‘›βˆ’π‘π‘œπ‘›π‘‘ precisely zero beyond pre-defined interatomic distance Shift method: modifies entire PES (downside: equilibrium distances slightly decreased) Switch method: modifies PES only over β€œwindow” (downside: too small a β€œwindow” can introduce strong, non-physical forces) Van der Waals: always used Electrostatics: sometimes used

9 Atom types Atoms classified by TYPE
Atom name Atoms classified by TYPE E.g. sp2 and sp3 carbons: different TYPES Parameters defined by TYPE Compromise between: Different properties for every conceivable environment (impractical) Only one property set per element only (too inflexibe) Atom type Topology file entry Carbon atom types (Parm22) Parameter file entry HA CT re (Γ…) Kb (kcal/mol-Γ…2)

10 B. Solvation Method 1: Periodic Boundary Conditions
Central box surrounded by neighbors Only particles in central box modeled explicitly Particles in surrounding boxes are images Forces on primary particles include interactions with images Several lattices available: cubic, truncated octahedral, … 𝐸 π‘’π‘™π‘’π‘π‘‘π‘Ÿπ‘œπ‘ π‘‘π‘Žπ‘‘π‘–π‘π‘  can be calculated without cut- offs using clever series expansion: EWALD method Cut-offs needed for 𝐸 π‘‰π·π‘Š

11 Method 2: Solvation Shell (β€œdroplet”)
Sphere of surrounding waters added to macromolecule Boundary potential (BP) restrains waters Trade-off: BP too small οƒ  waters ”evaporate” large οƒ  extraneous forces

12 C. MD Algorithms Begin with Newton’s equations of motion (1-D):
𝑭=π’Žπ’‚ 𝑭=βˆ’ 𝒅𝑽 𝒅𝒙 Integrate to solve for π‘₯ 𝑑 and 𝑣 𝑑 : 𝒗=𝒂𝒕+ 𝒗 𝟎 𝒙=𝒗𝒕+ 𝒙 𝟎 Discretize to create computer algorithm (Leap-Frog): 𝒙 𝒕+πœΉπ’• =𝒙 𝒕 +𝒗 𝒕+ 𝟏 𝟐 πœΉπ’• πœΉπ’• 𝒗 𝒕+ 𝟏 𝟐 πœΉπ’• =𝒗 π’•βˆ’ 𝟏 𝟐 πœΉπ’• +𝒂(𝒕)πœΉπ’•

13 Principles of MD MD Program Structure System Preparation Running MD Analyzing Results

14 Essential MD data structures
Parameter file Contains the force field: all bond, angle parameters etc. Topology file Contains data for essential moieties (amino acid residues, DNA bases, small molecules etc.): what is bonded to what, partial atomic charges etc. PSF Contains data for ENTIRE SYSTEM (amino acid residue or nucleotide sequence, solvent molecules; list of all bond, angle terms etc.) Coordinate file Contains x,y,z coordinates of all atoms in system

15 MD structure hierarchy for physical system
PSF Segment 1 Residue 1 Residue 2 Residue 3 Segment 2 Segment 3 Residue 4

16 MD anachronisms PSF originally stood for Protein Structure File (the early development of MD codes focused on proteins). But now used to describe any complete physical system. Residue originally indicated amino acid residue. But now refers more generally to substructures from which segments are made. Nucleotide in DNA Individual lipid molecule in lipid bilayer Individual water in set of solvating waters

17 Principles of MD MD Program Structure System Preparation Running MD Analyzing Results

18 Structure of macromolecule
X-ray crystallography Have to build some missing atoms, including almost all hydrogens Neutron diffraction Expensive (uses synchrotron radiation) but resolves the hydrogens Homology modeling

19 May need to complete or fix structure: Go through check list
Add missing hydrogens (most not resolved in X-ray diffraction) Add missing heavy atoms (occasionally not resolved) Choose between duplicate sets of atoms (crystal structure disorder) Adjust protonation states for pH being simulated

20 Adjust location of proton to create correct hydrogen bonding patterns
Where isoelectronic groups create experimental ambiguity, adjust for hydrogen bonding (affects His, Asn, Gln: 180o rotation may be needed)

21 Finish preparing system
Solvate (add waters) Make neutral (add counter-ions) Adjust ionic strength? (more counter-ions)

22 Summary of preparation steps
Create data structure Read topology file οƒ  Parameter file οƒ  Sequence Generate PSF οƒ  Patch to create disulfide bonds etc. Create coordinates Read coordinates from pdb file (X-ray) Build hydrogen coordinates οƒ  Add coordinates of other missing atoms Check structure Protonation states consistent with pH? Hydrogen bond patterns correct? Ambiguity due to isoelectronic groups (His, Asn, Gln)? Solvate & Neutralize Choose solvation method (periodic boundary conditions or β€œdroplet”) Add waters (PSF segment, coordinates) Add counter-ions to neutralize & adjust ionic strength

23 Principles of MD MD Program Structure System Preparation Running MD Analyzing Results

24 FLOWCHART OF AN MD SIMULATION
Initial Coordinates Minimize Structure Initialize Assign Initial Velocities Heating Dynamics Equilibration Dynamics Equilibration Phase No Rescale Velocities Stable? Yes Production Phase Production Dynamics Analysis of Trajectories Analysis

25 Judging stability during equilibration
Temperature steady or drifting? Energy fluctuations small (relative fluctuations < 10-4)? RMSD of coordinates steady or drifting?

26 Principles of MD MD Program Structure System Preparation Running MD Analyzing Results

27 Analysis Whatever you want! Equilibrium structure
Sampling of hydrogen bonding patterns Loop conformations Stability of secondary structure Opening or closing of channels Migration of small ligands …

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