Outline

Introduction

Terminologies

MD process

Analysis of trajectories

Short Practical session

 Introduction

Integrate Newtons 2nd law of motion for all atoms in a system

GROningen MAchine for Chemical Simulations

A versatile engine md simulations and energy minimization

Suited for biochemical molecules lipids, proteins, nucleic acids, polym

Outcome of an MD process
Molecular interactions
 Terminologies

Force field form & parameters of mathematical functions used to desc

All-atom
United-atom
Coarse-grained
Energy minimization non dynamical calculation of local potential ener
Steepest descent
Conjugate gradient
L-BFGS
Topology Complete descriptions of all atomic interactions in a system
 Terminologies (cont)

Equilibration solvent relaxation

NVT - canonical
NPT - isothermal-isobaric
NVE - microcanonical
Blowing up simulation failure
Inadequate minimization
Bad structure
Too large time step
Inappropriate pressure/temperature coupling
 Files

Input files
*.pdb Protein data bank (atom coordinates)
*.gro Gromacs format (atom coordinates + velocities)
*.itp atom information (charges, mass, radii)
*.top topology file
*.mdp MD simulation parameters
*.tpr run input file (all information for an MD run)
*.ndx index file {control operations (specify groups)}
Output files
*.trr trajectory (atom coordinates + velocities)
*xtc trajectory filr (atom co-ordinates ONLY)
*.edr trajectory file (energies)
Log CPU time, restart runs
 Scripts

Ionization (ion.mdp)

Energy minimization (em.mdp)

Temparature coupling (nvt.mdp)

Pressure coupling (npt.mdp)

MD real run (md.mdp)

Ion & energy minimization script
Nvt & npt ensemble script
Md run script
 Methodology Pre-MD

Starting structures
A protein PDB, Ligand PDB
Pre-MD process
Cleaning structures
Ligand topology external tools (PRODRG, ATP builder, ACPYPE)
Most challenging force fields cant handle foreign species (parametize)
Derive & validate force field parameters
Pdb-gromacs conversion
Use pdb2gmx top, itp and posres
Define pbc & solvate
Use editconf boxed.gro
Use genbox solvated_boxed.gro
Ionise Use genion ionised_solvated_boxed.gro
 Energy minimization & equilbration

Input files ionised_solvated_boxed.gro + topology

Energy minimization
Use grompp and mdrun em.gro

Temperature coupling
Use grompp and mdrun nvt.gro

Pressure coupling
Use grompp and mdrun npt.gro
 Final MD run & analysis

Input files npt.gro and topology

Production of a final md.tpr and mdrun

Use grompp
Mdrun md.tpr, md.trr, md.xtc, md.edr

Analysis First view trajectories

g_rms
g_rmsf
g_gyrate
 References

http://www.gromacs.org/
http://en.wikipedia.org/wiki/GROMACS
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/
http://md.chem.rug.nl/cgmartini/index.php/proteins
http://www.swissparam.ch/SwissParam_gromacs_tutorial.html
http://compbio.biosci.uq.edu.au/education/mdcourse/Analysis.html
http://ringo.ams.sunysb.edu/index.php/MD_Simulation:_Protein_in_Water
http://www.biocode.it/tutorial-mds-5.php