Editing VMD

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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. 

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== VMD Tutorial ==

[http://www.ks.uiuc.edu/Training/Tutorials/vmd/vmd-tutorial.pdf VMD Tutorial]

To open the main menu in some Linux PCs, you will need to type the command '''menu main on''' in the yellowish window. 

== Create Movies with VMD ==

'''Additional Software Required To Create Movies'''

 '''LINUX'''
 ppmtompeg included in [http://netpbm.sourceforge.net/ Netpbm Package Website]

 '''WINDOWS'''
 VideoMach 4.0.4. [http://www.gromada.com  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. [http://www.povray.org/download/ POV-Ray Website] 
 POV-Ray 3.7. BETA is also avaliable.

[http://www.ks.uiuc.edu/Training/Tutorials/vmd-ref/imgmv/imgmv-tutorial.pdf VMD Images and Movies Tutorial]

== Create MO plots with VMD & Gaussian ==

'''!!You need the formatted .fchk from Gaussian!!'''

To get it go to [[Cesca]], and [[G09]] for the tips on how to convert the .chk file in .fchk file.

Once the .fchk is done follow this process: 
  
Gaussian includes a standalone utility for generating cubs from the data in a formatted checkpoint file.[[http://www.gaussian.com/g_ur/u_cubegen.htm]].The utility is named cubegen, and it has the following syntax:
          
          cubegen 0 MO=n  file.fchk  file.cube 0 h

MO=n: Molecular orbital n. 
The keywords Homo, Lumo, All, OccA (all alpha occupied), OccB (all beta occupied), Valence (all valence orbitals) and Virtuals (all virtual orbitals) may also be used in place of a specific orbital number. There is no default for n, and an error will occur if it is omitted.

Then you can open the file with VMD and first get the geometry of your molecule. In a second step an isosurface with the positive and negative values of the electronic wavefunction or with the density can be added.

== Supported Molecular File Formats ==

 '''Molecule Coordinate/Structure File'''
 
 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'''
 
 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'''
 
 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. [http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD 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 

[http://www.ks.uiuc.edu/Research/vmd/current/ig.pdf Installation Guide]


'''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. [http://www.ks.uiuc.edu/Research/vmd/plugins/ 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\


== Unfixed Problems ==

Secondary Structure Plugin in LINUX version, it's not working properly because STRIDE code is unavaliable in 1.8.6. relase. So, use Windows version if you want to use this plugin. 

== "Word too long." bug ==
For some strange reasons, sometimes VMD cannot start and just show the message "Word too long.". To fix that just put this file [http://aliga.iciq.es/wiki/images/8/8a/Vmdrc.tgz .vmdrc] in your $HOME folder

== Links ==

[http://www.ks.uiuc.edu/Research/vmd/ Visual Molecular Dynamics Website]


== Current Versions ==

kimik.iciq.es - VMD 1.8.2 

* To use it, you will need to call the menu typing at the yellowish window: '''menu main on'''

tekla.iciq.es - It isn't installed.

infi.iciq.es - VMD 1.8.6 (only for pmiro user)

[[rigel.iciq.es]] - VMD 1.8.6 (only for esantos user)

[[rigel2.iciq.es]] - VMD 1.8.6 (only for pmiro user)

Desktop Computers - It isn't installed except for [[p019]].iciq.es - VMD 1.8.6, [[p024]].iciq.es - VMD 1.8.6 + plugins VASP, [[p030]].iciq.es - VMD 1.8.6 + plugins VASP