AIS-GRID LAMMPS and VMD - simulation and visualization of molecular dynamics

Official sites:

• LAMMPS

http://lammps.sandia.gov/

• VMD

http://www.ks.uiuc.edu/Research/vmd/

VMD

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.

Supported types of files

AMBER 4-6 structure file(.parm)

AMBER 7-9 structure file(.prmtop, .parm7)

AMBER 7-9 restart file(.rst7)

Babel file translator plugin

Biograf structure files (.bgf)

Insight II/Discover coordinate file (.car)

CHARMM coordinate file (.crd)

CHARMM, CNS, NAMD, X-PLOR PSF structure file (.psf)

GAMESS log file (.log)

Gromos 87, Gromacs structure file (.gro)

Gromos 96, Gromacs coordinate and trajectory (.g96)

H5MD plugin (.h5)

NAMD Restart file (.namdbin)

Insight II/Discover structure file (.mdf)

MMTK NetCDF structure reader (.nc)

Molden structure files (.molden)

PDB (Protein Data Bank) files (.pdb)

PQR (coordinate, charge, and radii) (.pqr)

SYBYL Mol2 structure files (.mol2)

Tinker coordinate and trajectory reader (.arc)

VASP atomic configurations (.POSCAR, .CONTCAR)

VMD XBGF structure files (.xbgf)

VTF structure files (.vsf, .vcf)

WebPDB (web-based PDB downloader)

XCrySDen, Quantum Espresso XSF/AXSF coordinate files (.axsf, .xsf)

XYZ coordinate files (.xyz)

AMBER 'binpos' trajectory reader (.binpos)

AMBER "CRD" trajectory reader (.crd, .crdbox)

AMBER NetCDF trajectory reader (.nc)

CHARMM, NAMD, X-PLOR "DCD" reader/writer (.dcd)

CPMD (CPMD trajectory) reader (.cpmd)

DLPOLY HISTORY file reader (.dlpolyhist)

Gromacs TRR/XTC reader (.trr, .xtc)

Gromacs TNG reader (.tng)

H5MD plugin (.h5)

LAMMPS trajectory reader (.lammpstrj)

MMTK NetCDF trajectory reader (.nc)

VASP trajectories of ionic steps (.xml, .OUTCAR, .XCATCAR)

VTF trajectory files (.vtf)

XCrySDen, Quantum Espresso XSF/AXSF trajectory files (.axsf, .xsf)

XYZ trajectory files (.xyz)

Autodock Grid Map File reader (.map)

AVS Field File reader (.fld)

Biomocca volumetric occupancy map reader (.bmcg)

Brix format electron density map reader (.brix)

CCP4, MRC format electron density map reader (.ccp4, .mrc)

Data Explorer (DX) format volumetric grid (.dx)

Delphi, GRASP unformatted binary phimap reader (.grd, .phi)

Delphi, GRASP formatted ASCII phimap reader (.big)

Gaussian "cube" file reader (.cube)

Molecular Discovery, UHBD GRID map reader (.grid)

gOpenmol PLT format electron density map reader (.plt)

"O" DSN6 format electron density map reader (.ds6, .dsn6, .omap)

Situs volumetric grids (.sit, .situs)

SPIDER volumetric images (.spi, .spider)

UHBD potential maps (.uhbd)

VASP charge densities and electron localization functions (.CHGCAR, .ELFCAR, .LOCPOT, .PARCHG)

X-PLOR, CNS format electron density map reader (.cns, .edm, .xplor)

XCrySDen, Quantum Espresso XSF/AXSF trajectory files (.axsf, .xsf)

XtalView "fsfour" electron density map reader (.fs, .fs4)

GRASP surface file reader (.grasp, .srf)

MSMS surface file reader (.face, .vert)

Raster3D scene reader (.r3d)

STL solid model triangulated geometry files (.stl)

Developed by University of Illinois at Urbana-Champaign

LAMMPS input file

LAMMPS

(units,atom style, read data or create atoms,simulation box, initialize particle velocities)

• Initialization

• Interaction

• Integrators

• Run parameters

(pair_style, pair_coeff, neighbor, neighbor_modify)

Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is a classical molecular dynamics code used as a parallel particle simulator at the atomic, meso, or continuumscale.

Demo

(timestep, type of time integration)

Ingredients:

• Initial configuration [r(t=0),v(t=0)]
• Interaction potentials [V(r)]
• a way to integrate F=ma

Laplace's Demon

Use cases

"We may regard the present state of the universe as the effect of its past and the cause of its future. An intellect which at a certain moment would know all forces that set nature in motion, and all positions of all items of which nature is composed, if this intellect were also vast enough to submit these data to analysis, it would embrace in a single formula the movements of the greatest bodies of the universe and those of the tiniest atom; for such an intellect nothing would be uncertain and the future just like the past would be present before its eyes."

Pierre Simon Laplace,

A Philosophical Essay on Probabilities.

• Material property prediction
• Biomolecular modeling
• Drug design
• High-throughput molecular screening

interaction

potential

Molecular dynamics

force acting

on the atom

acceleration

(number of timestep, frequency of thermo data printed, frequency of output data sent)

new

position

V -> F -> a -> r

Cumputer simulation method for studying the physical movements of atoms and molecules.

essentially

F=ma

Like a computational microscop

Developed by Sandia National Labs and Temple University

LAMMPS and VMD - simulation and visualization of molecular dynamics

Sergiu Busuioc

PhD at West University of Timisoara, Romania

Participant at SSP at JINR,2016