analysis of md trajectories - cineca · measuring chain flexibility rmsf is an analysis to measure...
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Analysis of MD trajectories
Tutorial 5Neva Bešker
High Performance Molecular Dynamics, Bologna, 2017
High Performance Molecular Dynamics, Bologna, 2017
Method:Molecular Dynamics
Properties:Structure and dynamicsThermodynamics
Systems:Molecules/Biomolecules in solutions
High Performance Molecular Dynamics, Bologna, 2017
How to run MD simulationsStep 1Obtaining a starting structure
Step 2Preparation of input data
Step 3Creating a simulation box
Step 4Adding a solvent
Step 5Energy minimization
Step 6Position-restrained Equilibration
Step 7Production runs
High Performance Molecular Dynamics, Bologna, 2017
How to: trajectory analysis
Two main groups of analysis
- Convergence/reliability analysis
- Estimation of system observables of interest
High Performance Molecular Dynamics, Bologna, 2017
Did we reach equilibrium…?
We need to make sure that all the chemical and physical properties of the system have reached an equilibrium, where their averages do not longer change as a function of time. A simple way to test this is by measuring the RMSD (root mean square deviation) of C carbon atoms position with respect to start.
Convergence/reliability analysis
High Performance Molecular Dynamics, Bologna, 2017
Equilibrium phase
Productive phase
Convergence/reliability analysis
RMSD
High Performance Molecular Dynamics, Bologna, 2017
High Performance Molecular Dynamics, Bologna, 2017
Measuring chain flexibility
RMSF is an analysis to measure the flexibility of the polypeptide chain. It calculates the fluctuation of C-alpha atoms coordinates from their average position.
For every atom one RMSF !
High Performance Molecular Dynamics, Bologna, 2017
High Performance Molecular Dynamics, Bologna, 2017
Loop
DBD domain
TET
How to: trajectory analysis
High Performance Molecular Dynamics, Bologna, 2017
How to: trajectory analysis
H bonds
High Performance Molecular Dynamics, Bologna, 2017
Secondary structure
How to: trajectory analysis
High Performance Molecular Dynamics, Bologna, 2017
Structural properties:Radius of gyration
Describes the overall spread of the molecule and is defined as the root mean square distance of the collection of atoms
from their common centre of gravity
How to: trajectory analysis
High Performance Molecular Dynamics, Bologna, 2017
Structural properties:distances
High Performance Molecular Dynamics, Bologna, 2017
Modelling of complex systems: where computation meets experiment
Pagina 16
Structural properties:Ramachandran plot
A Ramachandran plot is the projection of the structure between two residues on the two dihedral angles φ and ψ of the protein backbone
How to: trajectory analysis
High Performance Molecular Dynamics, Bologna, 2017
Structural properties:Ramachandran plot
High Performance Molecular Dynamics, Bologna, 2017
Thermodynamics: Potential Energy
Total potential energy (upper) and nonbonding (lower) – both in kcal/mol – as a function of the folding pathway for the three stranded B sheet peptide Beta 3s
High Performance Molecular Dynamics, Bologna, 2017
Thermodynamics: Heat capacity
High Performance Molecular Dynamics, Bologna, 2017
Thermodynamics: Free Energy
Biomolecular processes, such as folding or aggregation, can be described in terms of the molecule's free energy
High Performance Molecular Dynamics, Bologna, 2017