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'''Molecule Coordinate/Structure File Plugins''' | '''Molecule Coordinate/Structure File Plugins''' | ||
AMBER 4-6 structure file(.parm) | AMBER 4-6 structure file(.parm) | ||
AMBER 7-9 structure file(.prmtop, .parm7) | AMBER 7-9 structure file(.prmtop, .parm7) | ||
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XCrySDen, Quantum Espresso XSF/AXSF coordinate files (.axsf, .xsf) | XCrySDen, Quantum Espresso XSF/AXSF coordinate files (.axsf, .xsf) | ||
XYZ coordinate files (.xyz) | XYZ coordinate files (.xyz) | ||
'''Molecular Dynamics Trajectory File Plugins''' | '''Molecular Dynamics Trajectory File Plugins''' | ||
AMBER 'binpos' trajectory reader (.binpos) | AMBER 'binpos' trajectory reader (.binpos) | ||
AMBER "CRD" trajectory reader (.crd, .crdbox) | AMBER "CRD" trajectory reader (.crd, .crdbox) | ||
AMBER NetCDF trajectory reader (.nc) | AMBER NetCDF trajectory reader (.nc) | ||
CHARMM, NAMD, X-PLOR "DCD" reader/writer (.dcd) | CHARMM, NAMD, X-PLOR "DCD" reader/writer (.dcd) | ||
CPMD (CPMD trajectory) reader (.cpmd) | CPMD (CPMD trajectory) reader (.cpmd) | ||
DLPOLY HISTORY file reader (.dlpolyhist) | DLPOLY HISTORY file reader (.dlpolyhist) | ||
Gromacs TRR/XTC reader (.trr, .xtc) | Gromacs TRR/XTC reader (.trr, .xtc) | ||
LAMMPS trajectory reader (.lammpstrj) | LAMMPS trajectory reader (.lammpstrj) | ||
MMTK NetCDF trajectory reader (.nc) | MMTK NetCDF trajectory reader (.nc) | ||
VASP trajectories of ionic steps (.xml, .OUTCAR, .XCATCAR) | VASP trajectories of ionic steps (.xml, .OUTCAR, .XCATCAR) | ||
VTF trajectory files (.vtf) | VTF trajectory files (.vtf) | ||
XCrySDen, Quantum Espresso XSF/AXSF trajectory files (.axsf, .xsf) | XCrySDen, Quantum Espresso XSF/AXSF trajectory files (.axsf, .xsf) | ||
XYZ trajectory files (.xyz) | XYZ trajectory files (.xyz) | ||
'''Volumetric Data/Density/Potential Map Plugins''' | '''Volumetric Data/Density/Potential Map Plugins''' | ||
Autodock Grid Map File reader (.map) | Autodock Grid Map File reader (.map) | ||
AVS Field File reader (.fld) | AVS Field File reader (.fld) | ||
Biomocca volumetric occupancy map reader (.bmcg) | Biomocca volumetric occupancy map reader (.bmcg) | ||
Brix format electron density map reader (.brix) | Brix format electron density map reader (.brix) | ||
CCP4, MRC format electron density map reader (.ccp4, .mrc) | CCP4, MRC format electron density map reader (.ccp4, .mrc) | ||
Data Explorer (DX) format volumetric grid (.dx) | Data Explorer (DX) format volumetric grid (.dx) | ||
Delphi, GRASP unformatted binary phimap reader (.grd, .phi) | Delphi, GRASP unformatted binary phimap reader (.grd, .phi) | ||
Delphi, GRASP formatted ASCII phimap reader (.big) | Delphi, GRASP formatted ASCII phimap reader (.big) | ||
Gaussian "cube" file reader (.cube) | Gaussian "cube" file reader (.cube) | ||
Molecular Discovery, UHBD GRID map reader (.grid) | Molecular Discovery, UHBD GRID map reader (.grid) | ||
gOpenmol PLT format electron density map reader (.plt) | gOpenmol PLT format electron density map reader (.plt) | ||
"O" DSN6 format electron density map reader (.ds6, .dsn6, .omap) | "O" DSN6 format electron density map reader (.ds6, .dsn6, .omap) | ||
Situs volumetric grids (.sit, .situs) | Situs volumetric grids (.sit, .situs) | ||
SPIDER volumetric images (.spi, .spider) | SPIDER volumetric images (.spi, .spider) | ||
UHBD potential maps (.uhbd) | UHBD potential maps (.uhbd) | ||
VASP charge densities and electron localization functions (.CHGCAR, .ELFCAR, .LOCPOT, .PARCHG) | VASP charge densities and electron localization functions (.CHGCAR, .ELFCAR, .LOCPOT, .PARCHG) | ||
X-PLOR, CNS format electron density map reader (.cns, .edm, .xplor) | X-PLOR, CNS format electron density map reader (.cns, .edm, .xplor) | ||
XCrySDen, Quantum Espresso XSF/AXSF trajectory files (.axsf, .xsf) | XCrySDen, Quantum Espresso XSF/AXSF trajectory files (.axsf, .xsf) | ||
XtalView "fsfour" electron density map reader (.fs, .fs4) | XtalView "fsfour" electron density map reader (.fs, .fs4) | ||
Graphics Plugins | Graphics Plugins | ||
GRASP surface file reader (.grasp, .srf) | GRASP surface file reader (.grasp, .srf) | ||
MSMS surface file reader (.face, .vert) | MSMS surface file reader (.face, .vert) | ||
Raster3D scene reader (.r3d) | Raster3D scene reader (.r3d) | ||
STL solid model triangulated geometry files (.stl) | STL solid model triangulated geometry files (.stl) | ||
Revision as of 16:00, 1 June 2007
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
Molecule Coordinate/Structure File Plugins 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) 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)
Molecular Dynamics Trajectory File Plugins 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)
Volumetric Data/Density/Potential Map Plugins 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) Graphics Plugins GRASP surface file reader (.grasp, .srf) MSMS surface file reader (.face, .vert) Raster3D scene reader (.r3d) STL solid model triangulated geometry files (.stl)
How Install VMD in your Desktop PC
Download the latest version (1.8.6.) from VMD Website. VMD Download Website
LINUX VMD for LINUX OpenGL (Linux (Redhat 9 or later) with Mesa or hardware OpenGL) Unzip and untar the file in ./home/username/VMD/ Run VMD using vmd_LINUX executable. It is in ./home/username/VMD/LINUX/vmd_LINUX
WINDOWS VMD for Windows OpenGL (Microsoft Windows 2000/XP/Vista (32-bit) using OpenGL) Install MSI file using Windows Installer Run VMD
Environment Variables
LINUX VMDDIR : The directory which contains the VMD data files (such as this help file) and architecture-specific executables. By default, this is /usr/local/lib/vmd on Unix systems. VMDTMPDIR : The directory which VMD should use for temporary data files. By default, this is /tmp, or /usr/tmp on Unix systems. LD_LIBARY_PATH : On Unix systems add /usr/lib
Update Plugins
Download the latest plugins release (1.8.5) from VMD Website. VMD Plugins Download Website
LINUX Unzip and untar the file in ./home/username/VMD/plugins/
WINDOWS Unzip the file in C:\Archivos de programa\University of Illinois\VMD\plugins\
VMD Tutorial
Create Movies with VMD
Additional Software Required To Create Movies
LINUX ppmtompeg included in Netpbm Package Website
WINDOWS VideoMach 4.0.4. VideoMach Website We don't have a licence for this software, but there is a 30 days trial version.
Additional Software Required To Create High Definition Images
LINUX & WINDOWS POV-Ray 3.6. POV-Ray Website
VMD Images and Movies Tutorial