VMD

VMD is designed for the visualization and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer.

Supported Molecular File Formats

AMBER 4-6 structure file(.parm)

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

AMBER 7-9 restart file(.rst7)

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)

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)

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)

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)

Links

Visual Molecular Dynamics Website