VMD-L Mailing List
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About this archive
Starting: Thu Dec 19 1996 - 11:40:41 CST
Ending: Mon Dec 02 2024 - 12:22:13 CST
- ! Obtain degrees from Prestigious non-accredite dUniversities
- "'Hands-on" Workshop on Computational Biophysics at Pittsburgh, PA, May 21-25, 2018
- "adding polymer to CNT"
- "animate readdel"? (was: multiple automated calls to NAMD)
- "atomsel: set: bad data in 0th element" ffTK
- "can not find channel named ...
- "cartoon" failing to show secondary structure
- "cartoon" failing to show secondary structure--more info
- "color by mass" - change default colors
- "Determine file type" list is far too long...
- "Distributed Cavelib" VMD port
- "Draw" different things in different frames
- "Dynamic" gofr
- "Error: no indices found in file." in carma.indices using NetworkView
- "get {x y z}" returns single value
- "graphics top line" and "render POV3"
- "Hands-On" Workshop on Computational Biophysics
- "Hands-on" Workshop on Computational Biophysics at Lake Tahoe, August 4-8, 2014
- "Hands-On" Workshop on Computational Biophysics, July 6-10 and August 10-14, 2009
- "Hands-On" Workshop on Computational Biophysics, March 21-25, 2011, Atlanta, GA, USA
- "Hands-On" Workshop on Computational Biophysics, November 1-5, 2010 & November 29-December 3, 2010 in Urbana, IL
- "Hands-on" Workshop on Enhanced Sampling and Free-Energy Calculation at Urbana, IL
- "Hands-on" Workshop on Enhanced Sampling and Free-Energy Calculation at Urbana, IL, September 10-14, 2018
- "Hands-On" Workshop on QM/MM Simulations at Urbana, IL, April 5-7, 2018
- "Jump" in Energy and Volume graphs of my MD
- "Lines" representation does not show
- "Lines" representation does not show:remote
- "measure bond" vs veclength
- "measure fit" inaccuracy?
- "measure fit" problem
- "measure symmetry" and SymmetryTools fail to find simple symmetry
- "mol scaleminmax auto" vs. "mol scaleminmax $min_val $max_val"
- "no CUDA accelerator devices available", Nvidia GeForce 9600 GT card
- "non-grid" volumetric data
- "Not all atoms have unique coordinates"
- "nucleic" selection
- "OpenGL Display" and "VMD Main" windows; size and location on launch
- "pbcwithin" keyword
- "Pick item mode" inactive in OSX bundle ?
- "Prepare Parameterization from CGenFF Program Output" in ffTK
- "same as" failing?
- "Save coordinates..." silently overwrites existing files...
- "Selection not understood"
- "Sorry, this version VMD was compiled with Python support disabled"
- "spiral cylinders" instead of bonds when rendering with Tachyon?
- "tight" selection
- "transparent" material not working
- "truncate_trajectory" a new plugin
- "Unable to create OpenGL window"
- "user add key" feature
- "which files to make a spatial grid?" => Bug for list command?
- # of waters limit
- $64k/yr hpc post-doc@lanl
- %-sign shortcut for mouse->force->atom not working
- 'Abort file I/O' key not working
- 'gopython' Tkinter and Numeric Python error
- 'Hands-On' Workshop on Computational Biophysics using VMD and NAMD, February 11-15, 2012 in Urbana, Illinois
- 'Hands-On' Workshop on Computational Biophysics using VMD and NAMD, October 17-21, 2011, Bremen, Germany
- 'Hands-On' Workshop on Computational Biophysics using VMD and NAMD, October 22-26, 2012 in Urbana, Illinois
- 'Hands-on' Workshop on Computational Biophysics using VMD, NAMD, and ProDy, June 10-14, 2013 in Pittsburgh, PA
- 'percent' symbol syntax in .conf file?
- 'SURF' representation problem
- 'topology' command crashes vmd 1.8 (LINUX)
- 'within' command in VMD
- 'wrap' any kind of solvent
- (); [Fwd: PET force field & topolgy files etc.]
- (forwarded) cylinder drawing bug in 1.7b1 on NT?
- (forwarded) Modifying a Tcl script
- (fwd) vmd 1.7b1 sequence window disappeares
- (Minnesota Supercomputing Institute Install) VMD 1.9 beta 3 posted for download...
- (my) problems using molefacture dihedral
- (no subject)
- (Semi-)transparent windows on installation on a virtual server
- (UNCLASSIFIED)
- (xterm: Command not found) error
- -fpascal-strings flag when compiling with TDCONNEXION option
- -restrict option in measure sasa
- -samples flag of measure sasa
- .car or .xyz output
- .COOR TO PDB FILE
- .cshrc error prevents VMD working on OSX10.3.3??? or something else???
- .grd and .srf
- .gro files written with python script not displayed until strange modification
- .gro format to .pqr format
- .js file format for point cloud data
- .mdcrd to .trr conversion problem
- .obj Oddity
- .pdb file from XMD
- .pdbqt file type
- .psf and .params files for IMD
- .psf for porphyrin
- .str file generation of nitrile group containing ligands
- .trr files slow to load
- .VMD state file does not load properly
- .vmdrc
- .vmdrc file
- .xsf triclinic cell contents
- .xst file disagrees with pbctools/.dcd file - what are the limitations of pbctools?
- .xyz bond
- .XYZ File format
- .XYZ File format (DL_POLY conversion)
- .xyz file, namelist index too large error
- .xyz to .dcd using catdcd
- /usr/local/lib/vmd/vmd_LINUXAMD64: error while loading shared libraries: libOpenGL.so.0:
- 0ne of a kind repl1cas
- 1-Nanotube Zigzag and 2-saving coordinates problem
- 1.3b2
- 1.6.1 hotkey problem
- 1.8.2beta
- 1.8.3
- 1.8.5: VASP plugin not correct
- 1.8.6 install for Windows OpenGL (Microsoft Windows 2000/XP/Vista (32-bit) using OpenGL)
- 1.9.2 beta2 doesn't pop up window
- 1.9.3 Version
- 1.9.4 beta version of VMD
- 1.9.4_a43 mixes g++ and gcc during building and ignores LDFLAGS
- 1.9.4_a43 parallel build issues with high -j
- 1.9.4_a43: chemical2vmd should use /tmp instead of /usr/tmp
- 1.9.4a43-Catalina-Rev6 TkConsole Up Arrow History
- 1.9.4a50 - unable to open DCDs win64
- 100% of CPU usage
- 15% off on two watches
- 1999 VMD User Survey Report
- 1CA2 autoionization
- 2 Issues in VMD 1.9 beta3
- 2 more quick questions
- 2 questions
- 2 questions about "measure sasa"
- 2-Dimensional map of a lipid molecule around the protein
- 20 colors for 20 amino acids!
- 2000 VMD Survey Report is up
- 2006 VMD user survey in progress
- 2011 VMD User Survey results are posted...
- 2016 ISQBP Meeting: early registration / abstract submission deadline approaching
- 2D Contour plot
- 2D projection
- 2D RMSD matrix plot
- 2D rmsd matrix plot for C-alpha atoms
- 2D rmsd plot for C-alpha atoms
- 3 simple questions from a newbie
- 3-d printing of vmd scenes
- 3-d visualization
- 32bit memory problems on Mac OS
- 3D Connexion - Space Navigator (OSX drivers)
- 3D density in the specific part of the simulation box
- 3D glasses with LCD
- 3D Glasses with LCD for VMD
- 3D Graphics
- 3D grid data to 2D contour?
- 3D hardware
- 3d pdf
- 3D pdf problem
- 3D printing
- 3D projection of vmd window
- 3D projectors compatible with VMD.
- 3D protein visualization
- 3d space navigator and MacosX-vmd
- 3D Stereo : Windows 7, nVIDIA GEFORCE
- 3D texture mapping
- 3D visualization
- 3D visualization options on Linux boxes
- 3d visualization setup
- 3d visualization VMD / NVIDIA / Linux
- 3d viz?
- 3D-Connexion Space Navigator for Macosx
- 3D/stereo hardware recommendations wanted!!!
- 3dconnexion spacemouse pro and vmd on fedora 21
- 3Dconnexion SpaceNavigator (OS X)
- 3DConnexion SpaceNavigator in 1.8.7alpha30 on OS X
- 3Dconnexion SpaceTraveler works
- 3Dsig 2011: Structural Bioinformatics & Computational Biophysics, Vienna, 15-16 July 2011 (abstract deadline May 1st)
- 3Dsig 2011: Structural Bioinformatics & Computational Biophysics, Vienna, 15-16 July 2011 (abstract deadline May 1st).
- 3rd party tools- vmd
- 4x4 trafo matrices to get "homo-two-protein-complex"
- 64 bit NAMD on AIX and CatDCD
- 64 bit windows VMD
- 6DOF controllers
- 780Ti and NAMD2
- 7th Industrial Fluid Properties Simulation Challenge
- 99 Toyotas as low as 2% over invoice
- : about complexing protein and ligand!
- << Centering/aligning several molecules >>
- << Different values of RMSD >>
- << Hbonds distances >>
- << Loading trajectory file in Windows fails >>
- << memory issue? >>
- << multiple atom selection >>
- << thresholds for drawing bonds >>
- << Using CPK/Rasmol color scheme >>
- <<cionize on macOS error>>
- <<measure command>>
- <please insert a decent subject here next time, thanks>
- ??startup.command?? can??t be opened because CoreServicesUIAgent is not allowed to open documents in Terminal.
- ?Filesize limit exceeded (core dumped)? with VMD on Linux
- [AMBER] Viewing with VMD bonds set by the "bond" command
- [apbs-users] Missing library on mac
- [bigdcd.tcl] How to stream output to file
- [carlos.simmerling@gmail.com: ACS awards application announcements]
- [carlos.simmerling@gmail.com: ACS awards]
- [Contribute] transparent MacOS X icon for VMD
- [EXT] placing graphics objects at fixed locations on the display
- [EXT] Question for Installing Plugin for VMD on Mac
- [EXT] VMD for Mac stopped working after updating to Catalina
- [Fwd: pdb from trajectory] some clarification
- [Fwd: problems with manipulating control switches on VMS main menu]
- [Help] cross-sections
- [jfavre@cscs.ch: SC'15 Scientific Visualization Showcase]
- [jrodgers78@gmail.com: outputing secondary structure from timeline]
- [lammps-users] Initial configurations / topology for LAMMPS
- [lammps-users] LAMMPS to VMD: lmp2vmd tool
- [lammps-users] MDAnalysis (slightly OT)
- [lammps-users] NPT/ Missing bonds / atoms & atom overlap
- [lammps-users] Regarding rdf from VMD extensions+lammps
- [lammps-users] using topotools to view lammps output
- [linux-elitists] ATI Radeon support (fwd from deejoe@raccoon.com)
- [MMTK] Visualization to an image file (fwd from hinsen@cnrs-orleans.fr)
- [OT] pdb files with lots of residues
- [patch] Autodetection of formats supported by openbabel
- [patch] potential CUDA acceleration - load-balancing on different CUDA devices
- [phenixbb] secondary structure presentation in VMD
- [philippebopp@yahoo.com: PME calculations]
- [PyMOL] 3D on linux (fwd)
- [PyMOL] enable direct rendering DRI on fedora core 2
- [PyMOL] NVidia [7174] Drivers & Nuccyl
- [PyMOL] nVidia Driver 7664 for Linux
- [PyMOL] pymol crashes with new [7167] nvidia driver
- [request] Best practices for rendering frames and making movies
- [selection problem] When I choose all not 'solvent', one residue is gone?v1.8.3
- [Stefan_Franzen@ncsu.edu: Patch for deoxy and dideoxy nucleotides]
- [Tech] Colors in VMD
- [Tech] Customizing VMD: hot keys and popup menus
- [topotool] writelammpsdata : custom order for atom types
- [topotools]writelammpsdata
- [VMD TECH] Tracing VMD Variables (Part II)
- [vmd-l] Graduate assistanship in Bioinformatics at NCSA
- [VMD-NAMD] Question about Dipole of DNA / Dipole Moment Watcher Plugin
- [VMD] Cannot find "cionize" plugin
- [vmd] K3b bug?
- [vmd] max number of molecules on mac
- [VMD] Measure distance between two selections
- [VMD] Obtaining phonon spectrum of DNA
- [VMD] Power-spectrum calculation
- [vmd_chcwaaa@yahoo.com.cn: about measure dihedral angle]
- [VMDTECH] Drawing Methods, Part I
- [VMDTECH] Drawing Methods, Part II
- [VMDTECH] Hingefind
- [VMDTECH] Making Movies
- [VMDTECH] Morphing
- [VMDTECH] RMSD and best-fit alignments
- [VMDTECH] Schedule Change
- [VMDTECH] Secondary Structure
- [VMDTECH] Small things
- [VMDTECH] Smoothing Animations
- [VMDTECH] Tracing Atom Picks
- [VMDTECH] VMD 1.2b1 is now available
- [VMDTECH] Working with colors
- a air box
- a basic question on binding energy
- A box of amino acids
- A bug about "trans" command
- a common list problem
- a detail about PSFGENv1.4
- a display problem
- A error of " transforming dcd into pdb "
- a few questions about VMD
- a few questions on uninstall, labels, rasmol,seq window
- a file for commands of console
- A fill for "bodies" build out of surfacs
- a gas box
- a guide for installing vmd-1.8.7 on ubuntu10.10 (LINUXAMD64)
- a name quesiton
- A nanosphere with mass
- A patch for OFF import and a question about representation of surfaces
- A problem about atomselect command in a script
- a problem about multiplot
- a problem in visualizing dump files with vmd
- A problem on PBC
- a problem on Red Hat Enterprise Linux 5
- A problem on SASA measure
- a problem using python in vmd
- a problem with installation (to generate the Makefile )
- A query about the deletion of Hydrogen and re-adding them by psfgen
- a question
- a question about "measure fit"
- A question about atomic symbol and cell-border width using VMD
- a question about dcd files
- a question about force field toolkit
- a question about g(r)
- a question about get the coordinates in vector form
- a question about paratool
- a question about ribbon representation
- A question about the namd energy plugin of VMD
- A question about the plugin of salt bridge plugin
- a question in using PSFGEN
- a question regarding the signalproc package
- A question with dipwatch.tcl script in VMD
- a script for angular distribution
- a script to count the frames in which some water molecules interact with selected protein atoms
- a small bug in solvate 1.3
- a suggestion and query on command usage
- A very minor question on the MacOS X native bundle version
- A vmd bug 1.8a28
- a VMD script similar to "Rahmachandran plot' applicable to nucleic acids ?
- A VMD script to emulate the Matlab "jet" colorscale
- a water box containing only the absorbent heads of
- a way to create a nice image
- ABF Calculations Question 1
- ABF lowerboundary upperboundary
- ABF Question
- ABF tutorial: Methane-Hydration water going -> Water in gas phase?
- abinit plugin for VMD not yet tried?
- ABINIT plugin ready for testing: can read GEO and DEN files.
- abnormal water surface after nvt and npt for POPC membrane
- about ".cpmd" format
- About "Visualization and Analysis of CPMD data with VMD" tutorial
- about adding ions to an ion channel pore
- about analysis plugin
- About Atom Index Order
- about atomselect command
- about average structure
- about CHARMM electrostaic potential
- About CHARMM electrostaic potential map
- about CHARMM electrostatic potential
- About Cluster Plug-in
- about command measure dipole
- about command readpdb?
- about docking with VMD
- About drawing bonds.
- about dynamical change color of atoms
- About FFTP with transition metal complexes
- about frame
- about gamess plugin
- about graphics accelaration
- About Hydrogen bond calculation
- about inorganic builder and define variable
- About loading multiple XYZ trajectories
- about maximum number of atoms
- About mdffi cc
- about measure dihedral angle
- about measuring volume of the binding site
- about new vmd on windows
- About occupancy volume maps
- About open file .pdbqt in VMD software
- About openning a file to write in callback function
- about opls-aam ff for small molecules
- about parameter "wrapAll"
- about paratool
- About PLUMED with NAMD VMD
- About psf file
- about psf file generation
- about psfgen patch
- about resid
- about shape order parameter
- About snapshot rendering in VMD-1.9.2
- about superimposing by VMD
- About Tcl command
- about tcl program and run tcl script in namd
- About the criterion of H bond
- about the diffusion & msd plugin
- about the psfgen of vmd
- About the syntax in Autopsf - Add Patch for PRES PLIG
- about the wrap and unwrap by pbc plugin
- about TkConsole
- About using trace
- about viewing charge density
- about visualization in VMD
- about vmd
- About VMD compile in win32
- about vmd solvation plugin
- about writepdb
- absolute C.O.M motion calculation script: help
- Absolute ruler or position limits of the current view
- Absolute scaling? "Scale to #" does this?
- abuot avpos
- Accelerated MD (aMD)
- Accelerating your VMD 1.8.7 calculations with an NVIDIA Tesla GPU
- Access to bond information inside a VMD plugin...
- access to molfile plugin source code
- Access to Python libraries from Mandrake8.1
- Accessible volume around an atom
- accessing bonds angles dihedrals etc lists after PSF file is read into VMD
- Accessing Mapped Drive Files on iMac
- Accessing tachyon optix from commandline and dat file generation
- Accessing TCL through Python interface
- accessing values for selection keywords
- accessing VMD help
- ACE and NH2
- Acetone as solvent
- Acetylation AutoPSF
- ACS award information, Oct 15 deadline]
- ACS COMP awards announcement
- ACS COMP Division awards for Fall 2015 National Meeting in Boston
- ACS COMP Division student and junior faculty awards for Fall 2014 meeting in San Francisco
- ACS COMP division travel awards
- ACS COMP Division travel awards for Spring 2015 National Meeting in Denver
- ACTC Triangle Consolidation
- Action halted on error in ffTK: The following output QM was not recognized
- Activation energy
- actual simulation time for a frame
- acylated and amidated parameters.
- AD:Family Reunion T Shirts & More
- Adaptive real time selection and coloring in default display
- Add a gap in my simulation
- add a new color
- add a new file to vmd1.8.3 on linux(FC4)
- add a new file type to VMD on linux(FC4)
- add a new representation style to VMD
- Add a surface to a pdb file
- Add bond across boundaries
- Add H-atoms to Pdb file for NMR
- add Mg2+
- add new color index do VMD
- Add solvation box tool
- Add specific h-bonds
- Add Topology and Parameters in QwikMD
- Add transparent plane to molecular
- Add transparent plane to molecular structure
- Add user output to DCD trajectories
- add water on the top of protein border
- Add-H for crystallization water only
- Add/Remove Bonds
- add/remove bonds between different types of atoms
- Addforces
- adding 3rdparty plugins in VMD-1.9.1
- Adding a hydrogen through the command line and Molefacture
- Adding a keyword to mol addfile
- Adding a logo to a screenshot
- adding a metal ion
- adding a representation for a selection which is varying from frame to frame in a trajectory
- Adding a three letter residue name to VMD's protein recognition
- Adding a Water Box
- adding additional atoms to psf and dcd
- Adding an atom to existing trajectory (to enable RDF from centre of mass of a selection)
- Adding an atom to the existing pdb
- Adding an Implicit Solvation Compatible with below ffTK suggested Methods INQUIRY
- Adding Atoms in Colors Menu
- adding atoms to empty molecules
- adding atomselections?
- Adding bonds between many metal atoms
- adding bonds between segments
- Adding bonds in a script
- adding bonds with the mouse and writing psf
- Adding cadmium into protein
- Adding color scale bar on the screen
- adding free Fe(II) ions?
- Adding groups
- adding hydrogen atoms
- Adding hydrogens breaks "protein" atomselection and bonds
- Adding Hydroxide Ions to the simulation box
- Adding labels, etc.
- adding lipid bilayers
- Adding missing residues
- Adding missing residues to a protein
- adding modified residue into psf file from pdb
- adding new atoms to a molecule from a script
- Adding New Color Definitions to Color Form
- adding new colors
- Adding other online PDB data bases to VMD
- Adding oxygen molecules
- adding patches via autopsf
- adding residue at start or end
- Adding residues to dowser
- Adding Salt to a system
- adding selections
- Adding Single Residues to a Protein
- adding solvation box
- Adding Topology+Parameter For Small Molecule in QwikMD
- Adding two separate pdb files: Lipid Bilayer's with Protein's
- adding urea to a protein-water system
- adding water box
- Adding water in protein
- adding waters only in top of lipid
- addition on CHARMM electrostatic pot.
- Adjacent surface?
- Adjusting perspective
- Adjusting R/S configuration
- Adsorption and diffusion
- Adsorption VMD Tcl script error
- advanced python console
- advanced selections (or explicit pair list) for measure gofr ?
- Advantages of new RTX/Turing NVidia cards?
- advice for a PCI video card on redhat
- Affordable 3D stereo.
- again :resid of water that is H bonded
- again about average strutcure
- Aggregation analysis
- Alascan plugin error
- Alascan, psfgen errors
- alchemical transformations
- algorithm for command *within*
- algorithm for finding center of mass of the side chains in the protein
- Algorithm for RMSD and alignment
- Alias histidine residue
- Align a PORTION of several structures
- Align a trajectory
- align and superimpose crd structures.
- align axes
- align electron density map onto simulated structure (with different center)
- Align membrane
- Align mistake
- align molecules using "anchor" atoms
- Align only translation not rotation
- Align protein with different number of aminoacid
- Align specific residues of two structures
- align two molecules with index
- Aligning a dcd file of a protein consisting two chains
- Aligning Desmond Trajectories again
- aligning molecules with different number of atoms
- aligning molecules with modes from ProDy
- aligning multiple trajectories to a single .pdb file
- Aligning of ions and DNA
- aligning one molecule
- Aligning portions of proteins
- aligning protein based on one helix of protein
- Aligning structures
- aligning trajectories
- Aligning two proteins of varying atom numbers
- aligning- on top of the bilayer
- alignment
- Alignment and RMSD calculation
- alignment and rmsd fit
- Alignment issues
- alignment of two the same structures
- alignment problem
- alignment problem. trying to align new lipid to bilayer, but lipid always has wrong direction?
- Alignment Python
- Alignment with RMSD trajectory tool
- aligntool
- aligntool docs?...
- All that I never took the time to ask about VMD ...
- all within selection
- allowing negative 'resid' numbers in selection strings
- Alpha to beta conversion
- alpha-quartz with hydrogen bond
- Alpha-RMSD
- alter crosshair appearance
- Altering Definition of Molecular Coloring Method
- Altering extrabonds force constant during MD
- Altering water sphere and charmm type
- alternative display mode of HBonds
- altloc pdb entries
- AMBER (old ?) nucleic acids names not recognised
- Amber calculated structure(PDB) visualization in pymol vs chimera vs vmd
- AMBER coordinates with periodic box
- amber generated netcdf trajectories
- AMBER parmfiles
- Amber patches for Auto PSF generator
- AMBER pbsa electrostatic potential map
- Amber periodic images
- AMBER prmtop and traj to pqr - radii error
- Amber prmtop/inpcrd files
- Amber rst7 not loading
- amber traj to pqr - radii error
- amber trajectory
- Amber trajectory loading
- AMBER trajectory visualization
- Amber visualization problem
- AMBER6 format
- AMBER9 netcdf trajectory loading
- Ambient occlusion / Electrostatic surfaces
- Ambient/direct light missing after adding Glow lights to a tachyon scene with glow_lights.tcl
- AMD vs. nvidia support
- AMD64 vmd installation problems
- amd64/nvidiaFX1100/linux crash
- amidated C-terminus and pyroglutamate
- Amide peptide capping group lost in VMD
- amino acid mutation plugin
- aminoacid mutation
- Aminoacid selection
- ammonium sulfate ions in system
- Amorphous Structure code or builder
- Amorphous Structure code or builder for non-programmer
- An APBS problem
- an arrow for a dipole
- an continuous increased pattern for RMSD curve after long run
- an inconsistance between psf file and coor file after equilibration
- an old question
- an old...old..old..question
- An remark on PoV output
- Anaglyph rendering problem
- Anaglyph stereo with other colors
- analysing big trajectories
- analysing big trajectories (fwd)
- Analysis
- Analysis of DLG filles
- analysis of energy with water excluded from dcd file
- analysis script causes vmd to crash
- analysis scripts: VMD text /batch mode
- Analyzing a 10ns simulation on Mac aborts
- analyzing amino acids forming pore constrictions in a channel protein
- ANALYZING DESMOND OUTPUT IN VMD
- analyzing gromacs trajectories with VMD
- analyzing gromacs trajectory (.trr) with VMD
- Analyzing pdb files remotely with VMD installed locally
- Analyzing results of simulation done by gromacs
- Andres Morales sent you a little gift
- Android support
- Angle between a vector and a plane
- Angle between molecular dipole and nanotube axis.
- angle between protein domains:
- angle between two domains connected at a hinge
- angle between two vectors
- angle calculation trajectory
- Angle Cutoff variable for Hydrogen Bonds
- Angle parameters
- angles
- Angles and dihedral generation
- ANGLES and DIHEDRALS ... location in VMD code?
- angles and dihedrals in .psf file
- Angles between two groups of atoms
- Angles generated by AutoPSF?
- Angles in psf file
- Angular energy term
- Animate data
- animate delete
- animate error handling
- Animate Molekul
- animate read and write
- animate read command
- Animate the "beta" field
- animate transparency
- animate with varying atom numbers
- animate write of a selection in Linux version of VMD
- animated colors, trajectories, etc..
- animated gif
- animated gif option in VMD for Windows.
- animating an iso-surface
- animating drawn objects
- Animating Trajectories/NAMD Output files
- Animation
- animation and reps
- animation from files with different numbers of atoms
- animation of an atom diffusion inside a bulk crystal
- animation question
- animation with PDBs
- animation with variable number/names of atoms
- Animations using VMD:
- animations with molecular surfaces
- ANN: BioCoRE now includes remote job submission
- Announce VMD 1.9 released
- Announce: CPMD VMD visualization tutorial
- Announce: JMV version 0.7 is available!
- Announce: MDTools update
- Announce: New VMD Images and Movies tutorial posted online...
- Announce: new vmdmovie script available...
- Announce: Struc. Bio. Software DB updates
- Announce: Structural Biology Software Database
- Announce: Updated VMD 1.8 plugins available
- Announce: VMD 1.4 beta 1
- Announce: VMD 1.4 beta 2
- Announce: VMD 1.4 beta 3
- Announce: VMD 1.4 beta 4
- Announce: VMD 1.6 Released
- Announce: VMD 1.6.1 Released!
- Announce: VMD 1.6.1a2 is available
- Announce: VMD 1.6.1a3 is available
- Announce: VMD 1.6a1 is available
- Announce: VMD 1.6a2 is available
- Announce: VMD 1.6a3 is available
- Announce: VMD 1.6a4 is available
- Announce: VMD 1.7 Released!!
- Announce: VMD 1.7.1 released!
- Announce: VMD 1.7.1b1 test version is available...
- Announce: VMD 1.7.2 (Windows-only GUI update) is available
- Announce: VMD 1.7b1 is available!
- Announce: VMD 1.7b2 is available!
- Announce: VMD 1.8 is available!
- Announce: VMD 1.8.1 released!!
- Announce: VMD 1.8.2 released!!
- Announce: VMD 1.8.3 released!!
- Announce: VMD 1.8.4 Released!!
- Announce: VMD 1.8.5 Released!
- Announce: VMD 1.8.6 Released!
- Announce: VMD 1.8.7 released
- Announce: VMD 1.9.1 released
- Announce: VMD at Super Computing 99
- Announce: VMD Users Image Gallery
- Announce: ZoomSeq -- sequence browser for VMD
- Announcement about Faraday Discussion on Molecular Simulation and Visualization - call for abstracts deadline 22 July 2013
- ANNOUNCEMENT: BioCoRe
- Announcement: call for abstracts (**extended deadline**): SC15 workshop "Producing High-Performance and Sustainable Software for Molecular Simulation"
- Announcement: Hands-On Workshop On Computational Biophysics
- Announcement: QM/MM Workshop
- Announcement: User defined movie animation
- Announcement: Workshop on Simulation Based Drug Discovery (San Diego, CA, Sept 21-25, 2015)
- Announcement: ‘Hands On’ Workshop on Computational Biophysics (Berkeley, CA, Aug 3-7, 2015)
- Announcement: ‘Hands On’ Workshop on Computational Biophysics (Lake Tahoe, CA, Aug 3-7, 2015)
- Announcement: ‘Hands On’ Workshop on Computational Biophysics (Odense, Denmark, Oct 12-16, 2015)
- Announcement: ‘Hands On’ Workshop on Computational Biophysics (Pittsburgh, PA, June 1-5, 2015)
- Announcing MDSalon!
- annoying bug in 1.9.2
- Another feature request for vmd 1.8
- another tachyon problem
- Another thought related to drawing dipole moment vectors
- another trivial question regarding the key setting.
- antechamber for Windows
- antialiasing
- Antialiasing ?
- antialiasing problem
- Antw: Stereo Mode User Defined
- any body else have VMD problems with Linux + ATI FireGL X1-256p + fglrx-glc22-4.3.0-3.7.0
- Any interest in VMD supporting mirror reflections w/ ray tracing?
- Any Mac (Intel) users still running 10.4.x???
- Any methods for real stereo viewing with Mac and OsX
- Any TCL script to identify specific MD water molecules with their respective IDs, forming hbond with certain residues in every frame
- Any tutorial/manual for Dowser for membrane protein modeling
- Any way for comparing two structures??
- Any way to output contact map data
- any way to rotate and translate with mouse without changing modes?
- anybody interested in running VMD in parallel (without recompiling)?
- Anyone Completed ffTK Calc Bonded Tab using ORCA gbw instead of Gaussian chk?
- Anyone have catdcd-4.0 for BlueGene?
- Anyone have cyclic structures I can use for testing?
- Anyone using ATI X1600?
- APBS automation with VMD
- APBS data visualization
- APBS dx colors depend on order of molec files loaded???
- apbs electrostatics
- APBS electrostatics: Output file missing or unreadable.
- APBS error
- APBS error : Cannot read output file
- APBS for small molecules
- APBS installation problem
- APBS location in vmdrc ?
- APBS Output file missing or unreadable
- APBS plugin
- APBS plugin - lib error
- APBS Plugin for VMD
- APBS plugin requires molecule renaming after drag and drop loading of .pqr file
- APBS plugin, created file pot-PE0.dx
- APBS tutorial link broken
- apbs with vmd, no output
- APBS: ELEC values
- APBS: uncharged molecule
- apocynin/1k4u
- Apologies
- Apologizes for "How to select some sugar atoms"
- APPCRASH when loading a big trajectory file (.dcd) into VMD
- append glow lights to a VMD/Tachyon scene
- append pdb
- Appending to DCD file with "animate write"
- Apple hardware configuration
- Apple VMD not showing gro file properly
- Application Error message during dihedral optimization using FFTK
- Application Error while use of Auto PSF Builder
- Apply for ACS Comp travel awards for Spring 2017 meeting in San Francisco
- applying 6dof input forces
- Applying forces in VMD
- applying forces on a protein in VMD
- April promo on w4tches
- aquire coordinates from the points of the solvent representation
- Arbitrary values of isosurface
- Archived Spam in the VMD-L Mailing List
- area of protein cross sections
- area per lipid
- Area per lipid for tubular micellae
- ARM
- Artifacts in GLSL rendering mode: deformation and noisy shading of atom spheres
- Ask the Cluster Expert
- Ask VMD scripts
- Asking VMD to show bonds between periodic images
- Aspen Center for Physics 2013 Workshop
- Assertion failure OS X 10.14
- Assign active site
- assign bond color based on bond type
- Assign velocities so I can color by velocity
- Assigning Color Codes for stress/force in .xyz trajectory files
- Assigning colors to atom names
- Assigning different temperatures in the same simulaiton
- assigning segment id or a unique identity in lammps data file
- assigning variable names using a for loop
- assigning variables for representations
- assignment of "measure contacts" output to tcl variables
- Associating .crd file extension with COR Plugin
- Associating .crd file extension with COR Plugin.
- Asymmetric concentration gradient
- Asymmetric water molecule
- athlon64 version of vmd
- ATI 3.7.6 driver bugs (and VMD..)
- ATI crashes, use of setenv VMD_EXCL_GL_EXTENSIONS
- ATI fglrx 3.11 drivers for Radeon 8500 LE with linux 2.6 kernel, quad buffered stereo on sony G520???
- ati interlace mode
- ATI radeon 8500 and Linux quad buffered stereo
- ati radeon 9200
- ATI radeon x300
- atom coloring
- Atom distances from trajotory
- atom fitting in non-PDB order
- Atom ID Change
- Atom ID/Color change with timesteps
- atom index number
- atom index starting at 0
- atom indices from x y z coordinates
- Atom label offset
- ATOM LPH
- Atom movement within a range of Z value
- atom name can not exceed four characters in pdb and psf?
- Atom name label
- Atom names aliased after psfgen
- Atom names, RES-IDS...!!!
- ATOM or HETATM record
- Atom order in VMD
- atom position update for reference atom list
- Atom renumbering in DCD file
- atom selection
- Atom Selection & List Generation
- Atom Selection based on angular criterion
- Atom selection based on arbitrary columns in the pdb file
- Atom selection based on center of sphere
- Atom Selection for RDF
- atom selection from multiple molecules
- atom selection in cv module of VMD
- atom selection in vmd
- Atom Selection Rectangle
- Atom selection to identify residues that clash
- Atom selection with asterisk atom name
- Atom selections for measure - index sorting
- Atom Selections in QwikMD
- atom serial number
- Atom serial numbers in array format
- Atom sorting according to resid
- atom type
- Atom type information is not incremented after merging two molecules.
- atom types depend on PSF/PDB reading order
- Atom typing
- atom velocity arrows
- ATOM VELOCITY HIGH ERROR in Coarse grained Simulation
- Atomic bond counting wuth VMD
- Atomic trajectory to COM trajectory,
- AtomLexer/lex.yy.c error
- atoms deleted in patch try to come back
- Atoms dropped on running AutoPSF
- atoms filter?
- Atoms in rings
- atoms inside a Nanotube, Deleting
- Atoms moving too fast
- Atoms numbers in VMD
- Atoms on top of each in wrapped trajectory
- Atoms poorly guessed after applying a patch in Psfgen
- atoms selection
- atoms selection/special characters
- atoms with changing colors
- atoms within a radius cutoff and a percentage cutoff of a trajectory
- atomsel : setbonds: Need one bondlist for each selected atom
- AtomSel and Graphics
- AtomSel with object index (Python scripting)
- atomsel: writepdb failed for vmd 1.8.6
- atomselect
- atomselect across two different molids
- atomselect and macro
- atomselect counting
- Atomselect entire water molecule using pbwithin
- atomselect for interacting hydroxyl groups
- Atomselect in loops
- Atomselect in NAMD GUI
- atomselect moveby: non-numeric in vector
- Atomselect on several molecules
- atomselect one liner
- atomselect protein
- atomselect within
- atomselect within a loop
- atomselect: cannot parse selection text:
- atomselect: cannot parse selection text: index
- atomselection
- atomselection by wildcard and distance exclusion
- Atomselection for negative values
- Atomselection in NAMDENERGY
- atomselection in order
- atomselection near periodic boundaries
- Atomselection problem
- atomselection question
- Atomselection with the position selected conditions inside the loop is not working properly
- atomselection: number of residues
- attaching an arbitrary surface molecule to a nanopore
- Attaching NBD label to residues mutated to cysteine in VMD
- attachment file size limit for the mailing list
- attempting to source a script
- Attractive or repulsive with Namd Energy?
- Authentication error VMD-xplor
- Auto Bead Display Size using topotools
- Auto IMD
- auto ionise error
- auto none /psfgen
- Auto PSF problem with VMD 1.9.4a48-Catalina-Rev7
- Autobond Criterion
- AutoHotkey script for managing VMD windows
- Autoi::sod2pot problem in "Modeling Nanopores for Sequencing DNA" tutorial
- AutoIMD
- AutoIMD and fixedatoms
- autoimd error
- AutoIMD on VMD 1.8.3
- AutoIMD on vmd 1.8.6 IRIX....
- autoimd on windows
- AutoIMD with Periodic Boundary Conditions
- autoionization error in VMD
- autoionize
- autoionize "error procesing bonds"
- Autoionize / SODIUM
- autoionize adds too many ions
- autoionize behaviour on big systems
- Autoionize does not neutralize the system
- autoionize error in vmd
- autoionize not neutralizing the system
- Autoionize plugin
- autoionize plugin parsing error (vmd 1.9.3 )
- Autoionize plugin problem
- autoionize plugin..
- Autoionize question for DNA molecule
- autoionize script
- Autoionize with non water solvent
- autoionize with polyatomic ions
- automate pdb processing
- Automate QwikMD?
- automated loading
- automatic extraction of RMSD values of the heavy atoms of residues from NAMD output?
- Automatic loading of mol2 files
- automatic PSF builder
- Automatic PSF Builder Help
- Automatic PSF Builder on Windows
- Automatically shutting down VMD after NAMD terminates IMD connection
- Automatically zoom so that the protein fill the display
- automating graphic representations
- Automating VMD
- Automation of Analysis from QwikMD and Loading Trajectory Without Water in QwikMD
- autopfs: unknown atom type error when processing ATP
- autopsf
- Autopsf CGenFF input
- AutoPSF charge generation
- AutoPSF deleting residues
- Autopsf error
- AutoPSF error vecsub
- AutoPSF error with glycana (end of segment error)
- autopsf error: failed on end of segment
- AutoPSF errors
- autopsf errors in vmd1.8.5
- Autopsf Failed on end of segment
- AutoPSF formatted PDB: wrong residue order
- autopsf from console
- autopsf generator need at least one atom error
- autopsf needs at least one atom error
- Autopsf Not Generating Atom Numbers Beyond 99999
- Autopsf problem
- autopsf question
- autoPSF with a POPC membrane
- autopsf with many modifiers
- autopsf-patches C++ error 'expected integer but got "" ""'
- autopsf: can't read "logfilename"
- autopsfgen looking for wrong angle
- Autopsfgen verbose error output?
- autostereograms in VMD?
- Average angle between the lipid dipole vector and the bilayer normal.
- average area per lipid
- Average coordinates
- average pdb from dcd file
- Average pocket size?
- Average position of atom set
- average radius of cavity over many frames from hole
- Average strcuture
- Average structure
- Average structure and NamdEnergy
- Average Structure and RMSD
- average structure generation from trajectory
- average structure script
- Average structure using multiple frame trajectory
- average structure/solute and solvent
- average z-coordinate of a selection
- averaged structure
- Averaging volmaps
- Avoid atom indices reassignment
- Avoid vmd closing with script
- avoiding distance based bond search when reading a PDB file
- AVX512 support on Linux.
- AW: "OpenGL Display" and "VMD Main" windows; size and location on launch
- AW: A fill for "bodies" build out of surfacs
- AW: Accessible volume around an atom
- AW: Affordable 3D stereo.
- AW: Align only translation not rotation
- AW: Align specific residues of two structures
- AW: Animate Molekul
- AW: Antw: AW: Oculus Rift DK2
- AW: Any interest in VMD supporting mirror reflections w/ ray tracing?
- AW: Assigning different temperatures in the same simulaiton
- AW: Average structure
- AW: AW: AW: How to smooth atom labels in a MD trajectory?
- AW: AW: AW: VMD warnings
- AW: AW: AW: vmd-1.9.1 broken after upgrade to Ubuntu 13.10
- AW: AW: hydrogen bond criteria
- AW: AW: namd-l: FATAL ERROR: seek failed while writing DCD file: No such file or directory
- AW: AW: Simplest file format that includes atom color?
- AW: AW: The quality of movie made by VMD
- AW: AW: VMD warnings
- AW: AW: vmd-1.9.1 broken after upgrade to Ubuntu 13.10
- AW: AW: why vmd cannot load the dcd trajectory?
- AW: BUG(s): vmd-1.9.2b
- AW: BUG? Hbond rep brakes RowInterleaved Stereo VMD 1.9.2a35
- AW: Building NAMD 2.12 from Source with IB and CUDA
- AW: calculating total energy
- AW: Cannot start VMD in background from a script
- AW: Center camera rotation on a molid
- AW: Certain combinations of X-server and X-client do not allow VMD to start
- AW: Change bond per atom limit of VMD
- AW: Change transparency along a trajectory
- AW: changing chain id and pdb generating
- AW: code precision problem
- AW: coloring scheme in "VolumeSlice"
- AW: CUDA acceleration for Tachyon rendering?
- AW: Define the percentage of zoom
- AW: Defining a layer for a micelle
- AW: Display representations with Tk Console
- AW: Do I need a "professional" graphics card?
- AW: Does the VMD Linux 64-bit version perform better than the Windows 32-bit when visualizing large molecules?
- AW: Draw arrows in trajectory file
- AW: Error connecting to localhost on port 3000 and IMD connection ended unexpectedly; connection terminated.
- AW: Error: not possible to build nodeSelString: () and ()
- AW: Exactly align view direction to coordinate axes
- AW: Fast PBC wrapping in VMD
- AW: Feature Request: Stride on vmd commandline startup
- AW: fftk-charges
- AW: format I should use if I have different total number of atoms for each timesteps
- AW: Fwd: distance using pbc
- AW: Fwd: VMD 1.9.2 released!
- AW: Gaussian *.log/out visualize
- AW: Generating PSF for several proteins in one shot
- AW: Get num. of residues
- AW: get resname from resid
- AW: GPU accelerated MD
- AW: graphics in VMD and overlay
- AW: H-Bonds not shown when loading by topo readlammpsdata
- AW: HBonds Plugin - Hbonds criteria
- AW: hiding atoms outside the unit cell
- AW: how can we improve it in VMD?
- AW: How do I define "collision only" atoms using MSMS?
- AW: How to constrain a atom
- AW: how to control the superposition (measure fit) ?
- AW: How to create an aggregation of molecules with VMD?
- AW: how to enable multiple core rendering?
- AW: How to increase the number of core
- AW: How to make solid surfaces work with non-orthorhombic cells
- AW: how to make the structures in the movie look better
- AW: how to measure the thickness of the water shell
- AW: How to remove particular residues and then view "ramachandran plot" in VMD
- AW: How to smooth atom labels in a MD trajectory?
- AW: How to work on multiple pdbs by tcl script?
- AW: hydrogen bond criteria
- AW: ion visualization in VMD
- AW: IR Spectroscopy plugin questions
- AW: Isosurface Render - No Color?
- AW: issue drawing a PBC box centered on a selection
- AW: loading electron density maps with a script
- AW: loading trajectory
- AW: log colorscale
- AW: making a movie in a tcl script using graphics commands
- AW: making a movie of a atomselection of a very large trajectory
- AW: making self-adjustable high resolution images
- AW: manually change secondary structure
- AW: Measure Center Question
- AW: Measure Distance Script Question
- AW: measure Hbond and orient (with vec {0 0 1}) of a selected molecule
- AW: merging independent dcd files,
- AW: moving atoms and updating distances
- AW: NAMD 2.11 Cuda does not work with Quadro FX 3800
- AW: namd-l: Solvation in non standard solvent
- AW: namd2.exe has stopped working - NAMDEnergy
- AW: Native contacts tcl script crashed
- AW: new structure file
- AW: number of water molecules within 5 angstroms of the ligand
- AW: obtain a list of residue numbers
- AW: Obtaining VMD view matrices for tcl script
- AW: Oculus Rift DK2
- AW: pbc to keep membrane in center
- AW: pbc wrap -center com
- AW: PhD position in Computational Structural Biology at MPI Muenster
- AW: printing out trajectories with some random indices of atoms renamed frame by frame
- AW: Problem with assignation of secondary structure in VMD
- AW: Problem with Kinetic Energy of Atomselection
- AW: program errors
- AW: Protein went out of the Box
- AW: Quad buffered stereo from Quadro M4000 to HDMI monitor
- AW: query regarding phi-psi range for asigning secondary structure
- AW: Question
- AW: question about reading more volumes via atomselect or removing of them
- AW: Re-centering protein molecule
- AW: reg extracting coordinates for first water shell.
- AW: Reg: Peptide dimer
- AW: regarding the coordinate transformation on a curved surface to plane surface
- AW: Rendering snapshots
- AW: Residue numbers in outfiles PDB/GRO
- AW: RE: select all residues in a molecule
- AW: SASA area
- AW: Scale the molecule
- AW: secondary structure calculation at certain frame
- AW: secondary structure inconsistency
- AW: Secondary structure representation stays static
- AW: select all residues in a molecule
- AW: select atoms within a sphere - atomselect
- AW: Selecting atoms based on the charges
- AW: Selecting atoms of same type in a certain distance (between X and Y angstroms away)
- AW: setting up a 4k HD TV for passive stereoscopic 3d
- AW: Simplest file format that includes atom color?
- AW: Sodium within distance
- AW: speed of pbc join is slow
- AW: SScache performance; fast secondary structure assignment
- AW: Superimpose Models
- AW: Tachyon transparency and depth cueing
- AW: Tachyon-Optix failure when SSH X11
- AW: tcl command to write amber format files
- AW: tcl script for averaging a parameter along length
- AW: TCL script to track molecules moving within a specified region each time frame
- AW: Tcl scripting - Coloring residues by frame along trajectory
- AW: TCL scripting question: how to make a list of atomselections persistent?
- AW: The quality of movie made by VMD
- AW: the usage of measure bond
- AW: To the developers: Get current zoom value (scale)
- AW: To the developers: TCL implementation of autofit zoom
- AW: Transparency rendering by Tachyon
- AW: Unable to visualize my polymer chains generated using RIS theory using VMD properly
- AW: Userani.tcl script jumps frame after no play
- AW: veldcd file
- AW: Visualize a SMILES string
- AW: Visualize temperature
- AW: VMD 3D movies rendering
- AW: vmd and proxy settings
- AW: VMD crash on large DCD files.
- AW: VMD crashing when loading prmtop files
- AW: VMD TkConsole command
- AW: VMD warnings
- AW: VMD with 3D TV
- AW: vmd-1.9.1 broken after upgrade to Ubuntu 13.10
- AW: vmd-I: Fatal Error: Unable to Open CHARMM Parameter File
- AW: volumetric maps
- AW: water molecules amber force field
- AW: WG: vmd and proxy settings
- AW: WG: VMD mismatch between CUDA runtime and GPU driver
- AW: why vmd cannot load the dcd trajectory?
- AW: wrapper for VMD to read compressed .xz files
- AW: Wrapping problem
- AW: Writing DCD from modified coordinates
- AW: writing velocities from VMD
- AW: z-direction selection
- AW: Zoom-to-fit before rendering
- AW: zooming into a chosen atom
- Away from email until Sunday...
- Away from VMD-L/email until July 8th...
- Away until July 12, self-help encouraged!
- AWS for VMD and NAMD no longer working?
- Axes
- Axes are not rotated?
- Axes dilema
- B factor calculation
- B-factor Plot
- B-factor plugin
- Babel and VMD
- Babel and Windows
- babel compilation error
- backbone dihedral angles over trajectory
- Backbone representation of RNA
- backbone selection failing
- background color
- Background colour
- Background gradient in image
- Backspace and delete
- Backspace not functionning in console
- bad angels
- bad angels]
- Bad Length and GLXBadLargeRequest errors
- Bad performance of VMD
- bad resolution and too slow on mandrake 10.0
- bad text display in tk console (ubuntu 8.04 VMD 1.8.7 linux 32 bit)
- bad window parameter
- bad window parameter -- SOLVED
- bad_alloc error
- Bader Charge Analysis
- badwater script - help
- basal spacing
- base plane not being filled in for terminal adenines in ribbons/new ribbons
- bash calling multiple python scripts that open vmd pauses
- bash scripts quits after few frames
- Basic membrane plugin questions
- basic procedure for ABF-PMF calculation
- Basic question about improper
- Basic VMD questions...
- Batch image creation
- Batch mode on Mac OS 10.5.3
- batchmode use of "labels" functions?
- BB Trace
- Be someone whom you have never been before with DrMaxMan
- Be the largest man around
- Beginner with cyclic peptide
- Beginner's problem
- behavior of "mol addfile first/last" with non-integer frame numbers
- Behavior of TachyonLOptiXInternal Renderer
- best fit lines through two selections per each molecule ( I have 80 molecules) and the angle with another vector for each molecule
- Best fit plane axis
- Best hardware for 3d.
- best method for showing metal nanoparticle and protein in vmd
- Best VMD install for El Capitan OS X?
- Best way for model post processing?
- Best way to bond peptides
- Best way to extend molfile plugin
- Best way to join two PDB fragments by a peptide bond
- beta barrel structure generation
- Beta color of atoms
- beta column format in PDB
- beta column in a multiseq sequences alignment
- Beta testers wanted for modified AutoPSF
- beta version
- BFEE
- BFEE calculations for protein-protein complexes
- BFEE plugin error: 'measure center: bad weight sum would cause divide by zero'
- Big DCD file
- Big DCD file help
- Big trr trajectory
- bigdcd
- bigdcd + salt-bridge analysis
- Bigdcd - get coordinates from file
- Bigdcd and Namdenergy batch problem
- bigdcd for distance problems
- bigdcd v2.0 testers needed...
- bigdcd v3 available. testers needed.
- bilayer thickness in simulation of POPC membranes
- BIMac2019
- Binary request
- Binary VMD buid for Linux, text mode only
- Binding affinity simulation of a mutation structure.
- Binding free energy calculations
- Binding site similarity
- binning data for each frame and coordinate
- Bio-Image summer school in Paris this year
- BioCoRE Release: New Features
- Biometric Case Study Presentations Available (no charge), data mining and predictive modeling
- Biomolecular Simulations Meeting Bordeaux, 2&3 Sept. 2005
- Black & white VMD in CAVE?
- Black screen OPTIX interactive rendering
- black VMD opengl screen after replacing GPU
- blank output
- Blank thumbnails and non-working snapshots
- BMP snapshot
- BN nanostructure builder
- Body
- Bond angle distribution
- Bond between two hydrogen atoms
- Bond Colors
- bond connectivity for different frames
- bond connectivity not displayed in VMD
- BOND CP2 - CT2 IN PARAMETER FILES
- bond cutoff
- Bond display and Periodic Boxes
- BOND distance
- bond distance across different proteins
- Bond drawing questino
- Bond error
- Bond in pbc condition
- Bond information
- bond information in psf file
- bond Label position
- Bond Labels - Issue with Rendering
- bond length
- Bond Length and Bond Angle as a Function of Steps
- bond length definition
- Bond Lengths
- Bond lengths from PDB and PSF
- bond missimg
- Bond Optimization FFTK error
- Bond order cut-off value
- Bond representation of coarse grained molecules
- bond updating in VMD
- Bond/angle optimization using FFTK
- bonding across periodic boundary
- bonding across periodic walls
- Bonding energies between two atom selections
- Bondlength information!
- Bondlist limit
- bonds across periodic boundaries
- Bonds appearing as elongated lines
- bonds forming during simulation
- bonds in .psf file
- bonds in graphical representation
- bonds not created as desired
- bondsrecalc question
- Boolean operators and the new atomsel type
- boolean operators in graphics
- Boron nitride preparation
- boubt about consistency of measures
- Bounced VMD-L postings...
- Boundry Dimensions for Solvation
- Box boundaries displaying
- Box dimensions
- box information
- box information amber crdbox
- Box of non-polar solvent
- box vectores in .trr
- BPS Meeting @ Baltimore
- breaking a big dcd file
- Breaking a trajectory into separate files with tcl
- Breaking Bonds in VMD
- breaking the DCD file
- breaking the last bond when loading
- bridging_waters.tcl error and usage
- bring z-axis along a new vector
- Broken bonds in trajectory due to pbc
- Broken link to MacKerell parameterization tutorial
- Broken tube drawing method?
- Buffer Overflow in "label add" in VMD
- Bug fixed in volmap
- Bug in 'source' command or in for loop?
- Bug in AutoIMD
- bug in comments interpretation of vmd
- bug in Hbond Option
- bug in membrane plugin
- Bug in molefacture proline residue of official version (1.8.6 LINUXAMD64)
- bug in the g(r) evaluation?
- Bug in the tcl script
- Bug in VMD 1.9.3?
- BUG in VMD dx reader plugin
- Bug in VMD main?
- Bug in VMD-1.6 (linux, GL)
- Bug in VMD-1.8.7 multiseq functionality
- Bug in VMD?
- bug in xsfplugin [patch included]
- bug of VMD
- BUG Report -> Draw multiple frames
- Bug report for NAMDgui plugin in VMD (1.9.4 alpha 8)
- bug report in VMD 1.8.5
- BUG REPORT: Malfunctioning of VMD with Yosemite/ Follow up
- BUG REPORT: Malfunctioning of VMD with Yosemite?
- bug when starting VMD on MACOS ARM
- Bug with FEP?
- BUG with MODEL card in PDB file
- BUG(s): vmd-1.9.2b
- BUG: vmd-1.9.2 final Representations GUI
- bug?
- BUG? Hbond rep brakes RowInterleaved Stereo VMD 1.9.2a35
- Bugfix: new save_state.tcl for VMD 1.8 installations...
- Bugs ? Representation window does not update new material
- Bugs and Questions
- Bugs in solvate plugin
- Build a customized alpha helix using Molefacture by command
- Build a VMD forum?
- build dependency
- Build graphene sheets using VMD
- build unit cells and supercells for VASP
- build virus envelope
- Building a beta barrel using a beta hairpin
- Building a membrane
- Building a membrane from a individual surfactant molecule
- building a solvent/gas filled simulation box, no protein inside
- Building a sphere of atoms around a chosen atom
- Building Al2O3 or Fe2O3
- building amino acid modification
- Building amino acid simulation box.
- building an uncoming sulfide bridge
- building bilayer with DOPC or other lipids
- Building Boron Nitride
- Building HMMM using patch files
- building loops
- Building LPS membrane
- Building micelles
- Building NAMD 2.12 from Source with IB and CUDA
- building plugins fails on tcl based plugins
- Building Plugins to work with Mac Builds
- Building plugins with _USE_ZLIB (how to activate preprocessor macro)
- Building plugins with Borland Bcc32
- Building polymer psf from monomer topology
- building psf with CMAP, old topology remark entries still in psf
- Building structure
- Building unit cell from asymmetric unit
- Building VMD in Windows
- building VMD is tricky -please help
- building VMD on LINUX
- Building VMD on OS X 10.6 with Python and CUDA support
- building VMD on SGI IRIX 6.x
- Building VMD on windows 2000
- Building VMD under Windows 2000
- building VMD with opnempi support
- building VMD with Ubuntu 18.04
- Building zeolite cage
- Buried Surface Area
- by using Axel's HOOMD plugin, convert pdb to xml and missing bond information
- Bypassing MM parameterization of ligand in QMMM
- bypassing MolFrac step
- C atom projection calculation
- C NH1 C minimization error
- C-terminus link to side chain amine
- c_top2psf.pl
- ca contact map
- CA distance command
- CA-CA distances in a trayectory
- Ca-dist script
- caculate the RMSD of 10 DNA
- Cafe 1.0 plugin does not recognize commands
- CAFE plugin
- CaFE Plugin - Didn't Find vDW Parameter for Atom Type HT1 Error
- CaFE VMD Plugin Errors at PB Calculation Step
- Calculate accessible surface area
- Calculate angles using fit_angle.tcl
- calculate atom distance between two chain
- Calculate CC in MDFF
- calculate charges of the binding site residues with psfgen
- Calculate density
- Calculate End-End distance for DCD
- calculate end-to-end distance with trajectory files
- Calculate Free Binding Energy of Protein-Protein Complex: CaFE Extension
- Calculate Free Energy of Protein-Protein Binding
- Calculate Free Volume?
- calculate g(r)
- calculate HBOND
- calculate radius of empty space between selected residue
- calculate rmsd in a loop:feedback [sorry if you get it twice]
- calculate side-chain dihedral/torsion angles
- calculate structure of protein
- calculate the angle between two principal axes from two selecton
- Calculate the area of overlap?
- Calculate the bond and angle energy of a glucosidic linkage using NAMD Energy plugin
- calculate the percentage of beta-sheet and alpha helix with time evolution
- calculate the solvent molecule within a cut off from protein
- Calculate torsional angle with big_dcd adding a boolean control for pyrimidines and purines selection
- Calculate VolMap for every frame by a script
- calculate volume
- Calculating acyl chain order parameter profile on phospholipid vesicles
- Calculating and drawing symmetry axes
- Calculating angles between subunits
- calculating b-factors from trajectories
- Calculating Bias for Well-tempered metadynamics
- Calculating changes
- Calculating density for a molecule
- Calculating Diffusion Coefficient Using VMD
- Calculating dipole moment of protein
- calculating distance between center of geometry/mass of methyl hydrogens for all residue pairs
- calculating distance between center of mass of two set of residues
- Calculating distances from command line VMD 1.9.2
- calculating lipid order parameters
- Calculating mean square displacement and removing PBC
- Calculating minimal distance between two groups
- calculating number of water and osmolytes molecules at particular distance from protein surface.
- Calculating parameters in lipid bilayers
- Calculating pocket volume
- Calculating RDF from xyz file
- Calculating rdfs without the VMD gui
- Calculating residence time
- calculating RMSD for a trajectory file
- Calculating RMSD on two sets of points
- Calculating RMSF for a lot of trajectories
- Calculating RMSF plots without using scripts!!!
- Calculating system net charge with tcl in VMD
- Calculating the Tilt Angle of a non-helical peptide
- Calculating the torsion angles in nucleic acids
- Calculating time variation of potential.
- calculating total energy
- Calculating volumes enclosed by SAS
- Calculating volumetric data for a molecule
- calculation hydrogen bond.
- calculation limit of gofr?
- calculation of alpha helical content
- calculation of angular distribution function
- calculation of binding energy
- calculation of free energy between lipid membrane and protein
- calculation of geometric centers of the rings
- Calculation of gofr for non-orthorhombic boxes
- Calculation of ligand displacement Vs time
- Calculation of no. of turns, pitch in DNA
- Calculation of pair distribution function
- Calculation of residue pair energy values
- calculation of RMS values
- Calculation of RMSF
- calculation of rotation angle
- Calculation of VAF using signalproc plugin
- Calculation the Surface Area/Volume of a Protein Cavity
- Call for participation: ISQBP Meeting, Telluride 15-19.06.2014
- Call to Stride program failed
- Calling all DCD files in a directory sequentially using CatDCD
- Calling Python hackers....
- calling scripts from the command line
- Calling VMD from Linux Cluster
- Camera in VMD!!!
- camera navigator question
- camera position and scale
- Can a script change the projection?
- Can any of you help me out in building VMD pls
- CAN ANY ONE HELP ME
- Can anyone help me get the coordinate of the cylinders in the cartoon representation?
- Can anyone help me out with this script
- Can bonds radius be controlled by tcl command?
- Can Catdcd Write Out Periodic Cell Size Information?
- Can I build a structure by VMD?
- Can I calculate B-factor using VMD
- can I change the axes type to look like something like a graduated coordinate?
- can I combine several dcd files into one dcd file?
- Can I load NetCDF trajectories from AMBER in VMD on a Windows machine?
- can not compile VMD plugin
- Can not enter text in VMD plugin window
- can not import Hessian/charge from single point calculation
- Can not run VMD in interactive mode on the supercomputer from Mac
- can not visualize bond in vmd
- Can paratools really parametrize a structure? Is it really finished?
- Can specden produce the autocorrelation and not only the powerspectrum?
- Can the CG model built from VMD be used as an Input of NAMD,GROMACS and any other MD program?
- Can VMD add other organic solvent into system?
- Can VMD add other solvent except water in system?
- can vmd add protons to particular atoms?
- Can VMD build predicted protein structures by homology?
- can VMD display a box?
- Can vmd do symmetry operation?
- can VMD render movies in stereo quad-buffered mode?
- Can vmd select residues in radius of 3.5 to a specific residue?
- can VMD show artificial bond info?
- Can VMD show the interactions between different structure part?
- Can VMD visualize forces?
- can we control the number and distribution of solvate molecular
- can we delete in command line?
- can we export VMD scene as webGL file?
- Can we fix the position of two atoms while minimization?
- Can we get secondary structure from PDB files?
- can we visualize sos file?
- Can you show me an example of the .xyz file that is used to calculate the IR spectrum
- can't add packages
- can't build VMD on MacOs Ventura: use of undeclared identifier 'msms'
- Can't compile VMD 1.8.3: Tachyon 0.97 needed
- Can't connect to BioCORE
- Can't execvp vmd_SOLARISX86
- CAN'T FIND BOND PARAMETERS FOR BOND C - CPB IN PARAMETER FILES
- Can't find C-PDB bond parameters
- can't find file
- Can't import python math module
- Can't load a large dcd?
- can't read "::vmd_pick_event": no such variable
- can't read "viewplist": no such variable
- Can't read DCD files generated using NAMD.
- can't read pdb file
- can't see all frames in XYZ file
- Can't set graphics window position to 0,0
- can't use arrow key in vmd -disp text mode
- Cannot find "cionize plugin" in VMD
- cannot find PSF and PDB
- cannot ionize coarse-grained system
- Cannot load file for SASA analysis
- Cannot load Gromos96 trajectory file (attached)
- Cannot merge psf and pdb files using psfgen
- Cannot open parm7 file through tcl script, but can open via graphic interface
- cannot open vmd
- Cannot perform RMSD analysis
- Cannot read MSMS data files
- Cannot read MSMS facet file
- Cannot Remote Display on Ububtu
- Cannot Remote Display on Ubuntu
- Cannot run IED! :(
- Cannot show the simulation box
- Cannot start CAVE display
- Cannot start VMD in background from a script
- cannot visualize GROMACS trajectories in VMD 1.9.4 on MacOS Big Sur
- Cannot write parm7 file with type parm7
- cant connect Novint Falcon with VMD
- cant find output file from tachyon render.
- cant open .car file
- Cant start IED
- Cant use NAMDplot to plot
- capping or patching protein ends
- Capture query data
- capturing box dimensions from amber coordinate files
- Carbon Nanotube Interaction with Protein Simulation NAMD VMD
- Card for VMD with OpenGL & Linux
- Cardiolipin residue names changed by vmd
- carnal output trajectory
- Cartesian coordinates to polar coordinates
- cartoon of alpha carbon trace
- cartoon problems (encore)
- Cartoon represenation for non-standard residue
- cartoon representation
- Cartoon representation for large molecules
- Cartoon representation in VMD with amber netcd file
- cartoon representation of 1crn
- cartoon selection
- Cartoons and secondary structure prediction
- Catching error info before it shuts down ...
- catdcd
- catdcd - writing DCD with box info from namdbin and xsc files?
- catdcd -first
- catDCD 4.0 and xplor
- catdcd 5.1 not working from VMD terminal
- catdcd a vmd extension?
- catdcd and velocity dcd file
- CatDCD Desmond Support
- catdcd error
- catdcd error opening reading index file
- catdcd in VMD
- catdcd in Windows
- CatDCD on Windows
- catdcd plugin for Windows users
- CatDCD Question
- CatDCD refuses to work (mac)
- catdcd usage with Desmond trajectory
- catdcd vs readdcd.h error checking
- CatDCD windows binaries
- CatDcd Windows Version
- catDCD- convert DCD format
- catdcd.LINUX
- Catdcd?
- cave
- CAVE & Vmd
- CAVE and Flystick control
- Cave and usr keys defined in tcl
- CAVE on OS X
- CAVE Question
- CAVE Sensor Question
- cavetracker
- cavity/pocket representation
- CCL: show ruler in VMD
- CCL:md rookie update
- CCL:md rookie update (fwd)
- CCL:NAMD failure on Berendsen pressure scheme
- CCL:program for viewing MD
- ccp4 in vmd
- CD spectra
- CDROM/Windows/Linux
- CellPack
- Center a trajectory
- Center camera rotation on a molid
- center command
- center of mass
- center of mass 4 rdf VMD
- center of mass position
- Center of Mass RMSD in a trajectory
- center of unit cell
- center scaling and rotation
- center selection problem
- Centering an atom over the length of a trajectory
- Centering GPCR onto Lipid Bilayer
- Centering of the view on one atom
- centering problem in salvation box
- centering problem in trajectory tool
- centering seection on screen
- centering selection on screen
- centering the molecule
- Centering water molecules
- CentOS 6.4 crashed right after starting vmd
- Centre of gravity for movies
- Certain combinations of X-server and X-client do not allow VMD to start
- CG bead definition
- CG Builder
- CG builder for martini force field
- CG builder in script
- CG definition of POPS
- cg ionization
- CG lipid bilayer vmd 1.8.7
- CG Map Tool Syntax Error
- CG Martini File for Cholesterol
- CG- CNT
- cg_bonds.tcl
- cg_ionize
- CG_MD temperature
- cgenff atom type issue
- CGenFF atom types
- cgtools
- CGTools error: atom select: cannot parse selection text...
- CGTools Plugin
- CGTools with pdb and top files
- chain fails
- chain identifier change in the pdb files generated by the "solvate" and "Add Ions" plugin
- chain seprating and jumping because of periodic bound
- Chains x, y, and z cannot be selected
- Change atom color dynamically.
- Change Atom serial Atom
- Change atom types in topotools
- change axes name
- Change bond per atom limit of VMD
- Change browsing directory in mac
- change color from script
- Change color of drawn object
- Change Color Scale
- Change color scale data range
- change color sequence used in label graphs?
- Change coordinates
- change cylinder surface properties
- change default bond cutoff distance
- change default drawing and coloring method
- Change Font on VMD Main Window -- Linux
- Change in color of residue
- Change in reaction coordinate value after doing solvation from that of the crystal structure
- Change Label Font
- change location of temporay file storage (Win2k
- change location of temporay file storage (Win2k)
- Change of colour for bond distance
- change of font
- Change only the CA coordinates in a pdb file via tcl
- Change Path to Povray
- Change properties of representations - batch mode
- Change representation default from lines to points
- Change requested in lammps plugin for VMD
- change residue colors?
- change residue name and write a trajectory file
- change the radius of atoms
- change the representation of certain atoms which pass a geometric criterion during a movie
- Change Tkconsole brackground
- Change transparency along a trajectory
- Change VDW scaling in CPK drawing method
- change_tkconsole_color_of_background_and_foreground
- Changing a structure of macromolecule with VMD
- Changing alphanumeric atom naming scheme to numeric
- Changing atom colouring by a non-standard property
- changing atom number in animation
- Changing atom order in DCD structures?
- Changing atoms diameter
- Changing Beta values for each frame of a trajectory..
- changing bond color
- Changing bond numbers
- changing certain dihedral angles while keeping rest of molecule fixed
- changing chain id and pdb generating
- Changing color of a given atom
- Changing color scale bar location in VMD
- Changing colors
- Changing colors during a dynamics
- changing colours isosurface
- changing cpk shere scale in TCL
- Changing decimal places in a label?
- changing default colors for resname HIE HID HIP
- changing default sec struct colors
- Changing Default Settings for VMD Main Window
- changing dihedral angles in molefacture
- changing font size
- changing frame
- Changing Graphical Representations
- Changing isosurface wireframe thickness when rendering with Tachyon
- Changing isosurface wireframe thickness when rendering with TachyonL
- changing label format with some arithmetic
- Changing molecule number
- changing molid number
- changing name of N and C term residues
- Changing Nvidia driver
- changing occupancy for bunch of PDB file
- changing origin of rotation (NOT center of mass)
- Changing representations on a per-atom per-timestep basis
- Changing residue name for a resid
- Changing Text Style
- Changing the atom species during animation
- Changing the color of atoms of a particular name
- changing the color of Sn atom
- Changing the color of some atoms
- changing the color of subset of representation
- changing the default representation for the sequence viewer
- Changing the display window size in a script
- Changing the Font size of the XYZ Logo
- Changing the format of atom labels from %f.3 to something else
- Changing the Index values of a molecule (the differenece between gro and pdb files)
- Changing the label for resname
- changing the name of a residue
- changing the order of atom selections / alignment issue
- changing the representation of a vector
- changing the representation of all loaded molecules
- Changing the rotation and centering matrix of a molecule
- Changing the Secondary Structure of a Protein
- changing the tile angle of a peptide embedded in a membrane
- changing the tilt angle of a peptide embedded in a membrane
- Changing the title in the viewer window
- Changing Tk console background
- Charge coloring and Stereo hot keys
- charge exceed the range between Low bound and High bound in ffTK charge optimization
- charge information for the PMEpot plugin
- Charge opt in FFTK
- charge opt not converged
- charge optimization
- Charge Optimization error
- Charge Optimization error: error deleting "base-wat.pdb": permission denied
- Charge optimization in ffTK
- charge re-optimization
- Charge State Confusion
- charge surface area
- charge visualization
- charges in VMD 1.9 vs. VMD 1.8.7
- charges optimisation of a cationic molecule with ffTK
- Charlie Buy your loved one Hermes
- Charm force field for POPS lipid
- Charm++ fatal error: FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CG321 NG301 (ATOMS 6407 6408) .. ERROR) Error connecting to localhost on port 3000
- charm27 forcefield_topology
- charmm binary ele. pot.
- CHARMM CRD files: COR plugin
- CHARMM electrostatic potential
- Charmm expanded coordinate file format?
- Charmm FF parameter file for 2-hydroxypyridine
- CHARMM parameters for ADP-ribosylated arginine?
- CHARMM parameters for iodide and bromide
- CHARMM parameters for Mn 2+ ion
- Charmm parameters for Polybutylene terephthalate (PBT)
- CHARMM TO AMBER FORMAT CONVERT
- CHARMM to AMBER trajectory conversion
- charmm toppology : internal coordinates
- charmm vs amber
- CHARMM36 alleged missing CC CT1 NH2 angle params
- charmm36 and charmm27 together with namd?
- CHARMM36 and water: can the H-H "bond" be added to the wat.top file used by solvate.tcl?
- CHARMM36 topology files, AutoPSF and DNA
- charmm36 vs charmm27/22 topology
- charmmgen to autopsf
- ChatGPT knows basic VMD scripting...
- Cheap 3D Glasses
- Check and remove the overlapping between atoms
- Check DCD finish
- Check if the lysine residues are deprotonated or not inside the membrane ?
- Check out my photos on Facebook
- CHGCAR file read in VMD
- Child killed error: unknown signal
- chime vs vmd
- Chiral indices in VMD Nanotube Builder
- chlorine atom: Cl or CL ?
- chloroform box
- chloroform box ChARMM
- Chloroform Solvent Box
- Choice of a Linux machine for VMD and high-end computing
- choice of VDW radius
- Choosing an appropriate isovalue for comparing different systems
- choosing an optimal workstation video card for VMD
- Chromium
- CIF file reader
- Cionize
- CIonize Not Installed on Windows VMD
- Cionize on mac cuda
- Cionize plugin
- Cionize Plugin - Output Options?
- cionize plugin VMD
- Cionize question for DNA molecule
- cispeptide and chirality extrab options
- citing SODIUM program
- CL
- Cl ions
- Clarification on RMSF Calculation
- Clarification on solvent box sizing
- clarification to "problem using pbc wrap"
- classify and compute the forces between two atoms
- Classroom Stereo projection
- clear altloc field
- Clip
- clip plane and cpk / VdW
- Clipping plane
- Clipping plane redering issues
- Clipping plane tool and export
- clipplane
- Clonerep GUI issue with VMD CVS
- cloning a molecule
- Close contacts upon solvation of XYZ file.
- closewater.tcl
- Closing filehandles in vmd tcl script
- Cluster analysis
- Cluster Analysis given a dcd trajectory
- cluster of particles
- Cluster plug
- Cluster plugin and Gromacs g_cluster
- Clustering algorithm
- Clustering by RMSD
- Clustering MD trajectories
- Clustering plugin updated to v2.0
- clustering tool is not working
- Clusters help
- clusters visualization with colours
- CMAP and psfgen
- CMAP problem
- cmd line FFK
- CMYK
- CMYK images
- cns files
- CNT Analysis
- CNT structure formation
- Coarse Grain model for graphene
- Coarse grain modelling problem
- Coarse Grain Setup
- Coarse Grained - angle/bond parameters
- Coarse Graining Cholesterol with VMD's cg builder
- Coarse graining disordered protein
- coarse-grained solvate usage
- Coarse-graining a retro protein
- Coarse-Graining Protein with Ion Ligands
- Coarse-graining: Inability to assign charge to C-terminus using fix_martini_psf.tcl
- code precision problem
- colomb map in volmap tool
- Color a protein based on a property
- color atom by stress
- Color atoms
- Color bar
- Color bar in VMD
- color bar problem in VMD
- color by charge (can colors be changed?)
- color by frame?
- color by molecule number
- color by Name
- Color by position behavior
- color by resid
- Color by velocity (speed?)
- Color by volume
- Color by Volume on an Intel 945GM
- Color change in VMD
- color change on atoms selected using mouse
- color charmm dcd by kinetic energy
- Color code
- Color code the structure by RMSF values
- Color Coding by Residue Type
- Color error on loading
- color gradient based on the sequence
- Color of bond betwen atoms with different colors
- color problem with Ati Fire GL E1
- color problem with tachyon
- Color problem.
- color protein based on an event during a trajectory
- Color scale bar
- Color Scale Data Range
- Color scale data range for coloring by timestep
- color scale definitions with more than three colors?
- color sidechains differently
- Color specific frames with specific colors in a trajectory
- Color surfaces by electrostatic potential
- color the surface with electrostatic potential value
- color trajectory using specific values rather than color scale
- Color Transition in VMD
- color update for xyz trajectory
- Color wheel gradient
- color with name
- color: negative values
- colorid
- coloring
- coloring according to charge of residues
- coloring atoms based on max bond length; Need help with bond retrieval
- Coloring atoms based on timeframe range?
- Coloring atoms by a general scalar
- Coloring based on POS
- Coloring bonds in VMD
- coloring bonds on the same segments differently from those between segments
- coloring by atom type
- Coloring by BETA not updating per frame
- coloring by charge
- coloring by difference in beta factors
- coloring by gradient
- Coloring by RMSD during trajectory
- Coloring by type?
- Coloring different isosurfaces with user-defined colors
- coloring different polymers with different (random) colors
- coloring HIE, HIP, HID: sorry ... I got it
- Coloring lots of Groups
- coloring method
- coloring method User
- coloring method User for graphics like tubes?
- coloring method)
- coloring method: user
- Coloring mols by carbon only
- coloring names
- Coloring of a trajectory with atom types more than 9
- coloring of an item created by canvas
- Coloring of atoms/molecules
- Coloring of basins
- coloring of trajectory
- Coloring particular atom with particular index
- coloring residues with VMD
- Coloring rings with paperchain
- coloring scheme in "VolumeSlice"
- Coloring Scheme Spectrum
- Coloring Sections of Peptides
- coloring selected chains and residues
- coloring selection
- coloring surface by volume
- coloring trajectory depending on coordination number
- coloring waters
- coloring way in a volume slice
- Coloring with an XYZ file
- coloring.tlc script
- Coloring/material of ply files
- colormaps available for color by volume
- colors
- colors changed in animation
- Colors in VMd graphics
- Colour coordinating atoms in a trajectory by Coordination Number
- colour residues
- coloured surface
- Colouring
- Colouring Atoms according to the centro-symmetric parameter
- Colouring atoms according to their q4 or q6 values
- Colouring atoms individually
- Colouring atoms named with the same first letter
- Colouring by velocity component in VMD
- Colouring rings in paperchain
- colvars module
- Colvars module doesn't work
- colvars problem - different values in VMD and NAMD
- Combination of bigdcd.tcl and topotools plugin
- combine .pdb files to make movie
- Combine Drawing Methods - Cartoon and Disulfide Bonds
- combine together two PBD/PSF files
- Combine volmap occupancy maps
- combine.tcl
- combine.tcl error
- combine.tcl membrane plugin
- Combined "Within" atom selection
- Combining fragments for parameterization
- Combining multiple psf into one for collagen protein
- Combining PDB/PSF of Protein and CNT
- command args to MSMS in VMD
- command for volume slice?
- Command line argument
- command line dcd to trr?
- Command line for thickness parameter
- command line options for video in vmd
- command line rep creation
- Command line representation
- Command line troubles
- command measure inertia
- Command not found Error
- Command to change background to gradient
- Command to save visualization state.
- Commandline file processed before vmdrc read in
- Commands runs manually but not as a script
- Compare "measure rgyr" to SAXS
- Comparing distance.tcl/bigdcd.tcl with resid/CA vs index
- Comparing Structures with Multiseq and Qres
- Compatibility with Orcad (PSpice) ?
- Compilation
- Compilation and installation of VMD on Mac OS Catalina
- compilation error
- Compilation error: stride_LINUXAMD64', surf_LINUXAMD64, tachyon_LINUXAMD64 : No such file or directory
- compilation from source: first attempt failed
- compilation from source: make error message
- Compilation issues with tcl.h
- compilation of vmd 1.8.7 source
- compilation of vmd from source on armv8 RK3399 processor
- compilation problem using vmd1.8 alpha
- Compilation propblem
- compilation with python 2.5 and file permissions from the CVS repository
- compilation: forgot to say about Python
- Compile / Configure VMD with the Oculus Rift DK2
- compile a plugin source code
- compile catdcd.c
- compile error
- Compile from Source Crashes 5/11/04
- Compile of OpenGL shader vmdsphere failed
- compile problem for VMD1.8.6: OpenGLRenderer.C
- Compile VMD
- compile VMD 1.9 with FLTK 1.3
- compile vmd for windows 10
- compile VMD on freebsd 4.8
- compile VMD with cuda 6.5.14
- compile vmd-1.9.4a57 source - OptiXRenderer.h:84:10: fatal error: optix_math.h: No such file or directory
- compile windows binary in linux
- compiled failed
- Compiled version for MacOSX with non-standard options
- Compiling 64bit VMD
- Compiling CATDCD and VMD plugins on AIX5.2
- Compiling CUDAMarchingCubes.cu build error
- Compiling Fortran bindings for the VMD molfile plugins
- Compiling from source on Mac OS X 10.5
- Compiling NAMD from SRC: Tungsten@NCSA
- compiling on LINUXAMD64 problem
- Compiling on Windows
- Compiling plugins without netcdf
- Compiling plugins without netcdf support returns an error.
- Compiling problem
- compiling problems
- compiling stopped without any obvious erros
- Compiling VMD
- compiling VMD -- confused failure
- compiling VMD 1.8.3
- Compiling vmd 1.9 plugins
- compiling VMD 1.9.2 source with tcl 8.6
- Compiling VMD 1.9.3 64-bit on MacOS 10.13.6
- compiling VMD 1.9.3 under Ubuntu 22.04LTS: modern C library issues
- compiling VMD 1.9.3 with OSPRay support
- Compiling vmd for ppc linux
- Compiling VMD for Windows 64bit
- compiling VMD from CVS 2016 09 21
- Compiling VMD from source
- Compiling VMD from source on SDSC Datastar (AIX 5.2)
- compiling vmd from source--will that solve ied issue?
- Compiling VMD on IRIX 6.5 redux
- compiling VMD on mac
- Compiling VMD plugins on Windows?
- Compiling VMD under Windows XP
- compiling VMD with cuda from source
- Compiling VMD with full OpenGL
- compiling vmd with g++-4.6 on ubuntu
- compiling VMD with gcc 4.7
- Compiling VMD with the TNG plugin
- Compiling VMD-1.8 as a loadable python module
- compiling vmd...
- Compiling VMD: Trouble with DispCmds.C
- Compiling without graphics
- compiling/porting vmd
- complete residues within
- complex buried area
- compose pdb
- Compressed files
- compressed trajectory support
- Computational Biophysics Workshop using NAMD and VMD, November 18-22, 2013, Urbana, Illinois, USA
- Computational Electrostatics for Biological Applications (CEBA'13) July 01-03, 2013 - Genova - Italy
- Compute angle between 2 principal axis
- Compute B-factor from MD run
- Compute force between two atoms
- Compute the angle between a vector and the largest inertia axis
- Computer for 3D visualization
- Computer hangs on trying to launch VMD CUDA
- Computing angles
- Computing atom distances
- computing potential using pmepot
- Computing the transformation_matrix for best fit alignment of structures
- concantenating psf files
- Concatenate DCD Files with Different Numbers of Atoms
- Concatenate Outputs
- concatenate protein and 2 ligand files
- Concatenate translated pdb's in to one pdb file- Writepdb is giving error
- concatenate two pdb files?
- Concerning protein rotation
- CONECT in pdb files
- CONECT Records in .pdb file - bonds not getting plotted
- conect2psf
- Confidential
- Configuration file
- configure do nothing (Linux)
- configure do nothing in Linux (???) - thank you !
- configure do nothing in Linux(???)
- Configure VMD while GROMACS Installation
- Configuring Tkcon in VMD for Catalina to access history with up arrow
- configuring vmd w/ browser on OS X
- conflict between VMD and Cygwin
- conflict between VMD and Netbeans IDE on MacOSX
- Conformation assignment
- conformational alignment
- conformations of a linker
- confusing about the residue number
- connect a spring between all the atoms present in pdb structure
- Connect particular residues with a line
- Connecting a phantom with NAMD and VMD
- Connecting new residues to old residues in topology file
- Connecting VMD to a supercomputer center
- connectivity in RBCG file(pdb extension)
- Connectivity lost when loading second pdb
- connectivity problem
- Consider fluctuating volume for density
- Considering special bonds not all of bonds,
- Consistent size
- console in vmd-1.8.3 amd64 is blank (like white text on white background) so I can't see any output messages
- Constant pH MD with NAMD
- constant region selection for animation
- constant velocity for carbon nanotubes
- Constraining two sets of atoms
- constraints
- constructing a .tpr
- constructing spherical molecule?
- consultation about metal_enviroment.tcl
- contact between 2 residues
- contact map
- contact map (over all frames)
- contact map definition
- contact map for Protein-DNA interaction
- contact map in Rainbow scale
- contact map lig-pro
- Contact map using VMD Contact Map Plugin
- contactmap for RNA
- Contacts among two sets of atoms
- contacts and pbc
- contactvFreq TCL script not running
- contour plots
- Contour plots for XYZ format
- Contribution of selected atoms to surface
- control drawing method
- Control of aminoacid ionization in VMD
- control the spacing between the dashes in the hydrogen bonding between two atoms
- Convergence of the Gram-Charlier expansion
- conversion from CHARMM27 psf to charmm36 with psfgen?
- Conversion from gromacs trr trajectory into charmm trajectory
- Conversion into POVRay coordinates
- Conversion of DCD trajectories to AMBER ones ?
- Conversion of GAMESS Quantum MD trajectory file
- conversion of gromacs trajectory file (xtc) to amber trajectory file (mdcrd)
- conversion of topology entries from charmm str format to vmd psfgen format
- Conversion of trajectory files
- conversion of vmd generated (C36) bilayer to gromac format
- convert .coor to pdb
- convert .mrc map to .dx format
- convert AMBER format file to CHARMM format file or NAMD format file
- Convert an ascii matrix to an image
- Convert CHARMM psf to X-PLOR
- convert dcd file to xyz
- convert DCD files to GROMACS .XTC format
- convert dcd to coordinate, each frame, conserving the identity
- convert frames to nano seconds
- convert pdb file from angstorm to nm units
- convert PDB file to CRD?
- convert pdb format to normal pdb format
- convert pdb to psf
- convert prmtop to psf
- Convert problem
- convert psf to top with topotools
- Convert RNA to DNA
- convert tcl to python
- convert THR and SER to the phosphorylated forms
- Convert trajectory
- convert unformatted delphi phi to formatted
- convertind dcd to xyz file
- converting
- converting .dx volumetric data to 2D isocontour
- Converting .txt trajectory files to VMD compatible format
- converting a .cif file into a vmd readable format, how?
- converting coarse grained POPC membranes to atomistic representation (AMBER, GAFF)
- converting Desmond trajectory and energy file to gromacs
- Converting electron density data from .map to .dx in vmd
- Converting electron density data from .map to .dx in vmd Faisal, H M Nasrullah
- Converting Files with VMD
- Converting graphics to a pdb's coord system
- converting NAMD trajectories
- Converting namd trajectory to desmond trajectory
- converting old LAMMPS ASCII dumps
- converting pdb to xtc
- Converting tracker coordinates to molecule coordinate for selection
- converting trajectory files with catdcd in command line
- convex hull and VMD
- coordinate translation
- COORDINATES extraction of molecule's centers of mass
- coordinates of an atom
- coordinates with get command
- coordinates: visual and in-file
- CoordinateTransformation
- Copying a selection
- copying parts of an atomselect selection
- Copying the new alpha sources of VMD into the installation directory
- COR format and first residue
- COR plugin for SGI
- core API?
- core dump
- core dump when launching vmd1.8a21
- core when using some features of vmd-xplor
- correct "origin" in VMD
- Correlated motion
- correlation
- Correlation Functions
- Correlation matrix illustration via heating map
- corrigendum: error when solvating a system
- Corrupt cpmd-vmd.pdf File?
- Could not load .nc file in MAC installed VMD
- Could not locate 'dowser' (Program not found message box)
- could not make avi file
- could not read file no atoms found error
- Could not read file problem
- could not visualize DCD file downloaded from VMD website
- couldn't execute "psfgen": no such file or directory
- couldn't fork child process: not enough memory
- Couldn't load the trajectory on to vmd
- Couldn't locate ppmtompeg
- couldn't open "c:/multiseq-406080740227.start.domain": invalid argument
- Couldn't open required GL library
- Couldn't read internal coordinate table and list index out of range
- count CLA number from different frames
- count variable number of molecules
- Count waters inside a specified box
- counting gas molecules inside the nanotube
- Counting H-bonds from a dcd file
- Counting number of hydrogen bonds in the representation
- Counting number of water molecules
- counting selected atoms---selection time series
- counting specific atom types
- Counting the number of ligand molecules around my protein
- Counting water transition through a channel
- covalent atomic radii customization
- covalent bond
- covalently bonded atoms
- cp: cannot stat `../LINUXAMD64/vmd_LINUXAMD64': No such file or directory
- CPK Graphical Representation
- cpptraj-nastruct + VMD
- CPU comparison
- Crack generation in Grapehene sheet
- crash on ubuntu linux
- crash with 1.9.2 and not with 1.9.1
- Crash with molfile plugin when doing "Load data into molecule"
- Crating 3D PDF files
- CRD problems and CRD to DCD conversion
- Create a new color category
- Create a PSF
- create and operate a point in space
- Create atom selection from list of integers
- Create Binding Pocket of Every PDB File In A Directory Using TCL Scripts and Atomselect Command protein and within 4 of resname LIG
- Create bonds in VMD
- create bonds with uniform pairwise cut off radius for XYZ trajectories.
- Create CHARMM COR files with VMD
- Create covalent bonds between 2 atoms via Tk console
- create images in vmd
- create movie from multiple frames
- Create multiple tcl interpreter child instances within VMD to run several scripts at once
- Create new atoms
- create new colors
- create new topology file for new molecule
- create new topology file for new molecule]
- create psf and dcd from pdb
- create psf file without hydrogens
- Create Straight Peptide Molefacture Protein Builder
- create surface of overlapping VdW volume
- Creating 3D PDF files
- Creating a .tpr file from NAMD files Error
- Creating a constraints file(.pdb) from NMR constraints file(.mr)
- Creating a cuboid box to fit in atoms
- Creating a demo - updating the OpenGL window
- Creating a fragment of the given protein
- creating a modified pdb/psf file
- Creating a pdb of periodic images of a unit cell
- creating a povray file
- Creating a Regular Structure
- Creating a VMD movie from a Tcl script
- creating an index file for POPC in water
- creating and appending to DCD in VMD
- Creating and using a tk button
- Creating AVI movies
- Creating bond between two atoms
- Creating bonds using VMD
- Creating boxes of different water models
- Creating Carbon Nano-tube psf file..
- creating chiral molecules
- Creating custom molecule in VMD scripting
- Creating data file for triclinic system
- Creating Dummy Atoms in VMD Using TCL Script
- creating gif animation with povray
- creating high quality movie in VMD
- Creating length dependent coloured bonds in VMD
- creating model helices
- creating movie files
- Creating multiple views from same trajectory file for movie generation
- creating nonstandard solvent
- Creating PDB files of binding pockets that lists ligands first within the file
- creating periodic images of an atom
- creating psf file
- Creating psf file for graphene sheet
- Creating PSF from PDB files
- creating psf from pgn
- creating psf with trimethoprim
- creating scripts
- creating SiO2 device with Inorganic Builder
- creating spherical water droplet
- Creating surfaces with desired lengths- Inorganic Builder
- creating the center of mass pdb file
- creating topology for a unique structure
- Creating very large solvation boxes
- creating videos where the representation changes throughout
- Creating VR-movies with tachyon renderer
- creation of psf
- Creation of SiC NP
- Creation of Thin Amorphous SiO2 using Inorganic Builder-VMD
- criteria for detecting hydrogen bonds
- criteria for hydrogen bonds.
- cropping the missing residues from other PDB file
- Cross correlation
- cross correlation in VMD
- Cross-correlation coefficient calculated MDFF package
- Crosseye stereo image rendering
- crystal eyes vmd
- Crystal water
- crystallographic symmetry tool
- cube file question
- cube file: coordinates rotated
- Cube Files - proportion of the electron density
- CUBIC box of system
- CUDA 10
- CUDA acceleration for Tachyon rendering?
- Cuda an a cluster ?
- CUDA cores seen by VMD on GT540M
- CUDA driver for Mac OS X 10.7 on Late 2008 13 inch Macbook with NVIDA GeForce 9400M 256 MB ?
- CUDA Error with Quicksurf
- CUDA error: an illegal memory access was encountered, CUDAQuickSurf.cu
- CUDA errors for graphics card in Linux
- CUDA issues
- CUDA out of memory
- CUDA Support
- CUDA-NAMD hangs -- check the Northbridge temp!
- Curious about analytical capabilities of VMD
- cursor size/shape in pick mode
- custom color on surface plot
- custom db in Multiseq
- Custom particle shapes
- Custom residue in mutate psfgen
- custom residue ribbon/cartoon representation issue
- Custom selection variable
- Custom Visualization of Atom Properties Change with Color
- Custom VMD script development service for fee
- Custom Water Box
- Customized radii
- Customizing vdw radius
- Customizing VMD Sessions
- Cutting a bond
- Cutting a sphere with a specified radius along a trajectory
- Cutting and replacing in VMD
- cutting short a DMPC bilayer in VMD
- cvs
- CVS access is back online...
- cvs plugins do not compile because of errors in the sgsmooth.C
- CVS root directory not found
- Cyclic peptide Nanotube
- Cyclic peptide nanotube psf second mail
- cyclic peptides
- Cycling between files using the same output file
- cylindrical water
- Cylindrical water box
- Dangerous bug with pbwithin selection?
- Dangling Bonds
- data analysis script help
- Data fields in vmd
- data file extensions
- DCD architecture dependence
- DCD Based on a parameter
- DCD command-line options
- DCD file
- dcd File and bounds
- dcd file appears to contain no timesteps
- dcd file error
- DCD file format
- DCD file format?
- dcd files generated with catdcd
- DCD for windows
- dcd format
- dcd header information missing
- DCD is not detected as protein but single pdbs are?
- dcd large files, charmm-VMD
- DCD Question
- dcd reading error
- dcd reading routines
- dcd to coor files
- DCD to XYZ conversion)
- dcd tools
- DCD unit cell data
- dcd with fixed atoms
- DCD write/save with a python script
- dealing with large pdb files
- Dealing with lone pairs in fftk
- debug
- debugging tool for atomselect
- Decompose Transformation Matrix to Rotations and Translations along XYZ axes
- Decrease in CC during MDFF
- default colors
- default directory
- default drawing style
- Default parameters for image renderers
- Default radii and colors
- Default representation style in command line
- default representations for multiple molecules
- Default resource file (.vmdrc)
- Default XML format
- Define "color Element" through rgb values
- Define bond length
- define custom colours for posX gradient
- Define the percentage of zoom
- define water cavity using atom selection in graphical representations window
- Defining a layer for a micelle
- defining bonds
- Defining Bonds in .xyz file format
- Defining graphics colors
- Defining space coordinates for multiple structures
- defining/updating atom selection within loop
- definition of single word "protein" selection
- defintion of alpha helix in vmd?
- delatom "no segment..."
- delatom usage - no such segment?
- delet a frame from dcd file
- delete angle type with topo tool
- Delete atoms from selection
- delete bad atom in psfgen
- delete bonds in TIP3P
- delete bonds in TIP3P water model
- Delete frames in a script
- delete of some molecules
- Delete overlapping residues
- Delete redundant bonds in water molecule
- delete residues from trajectory
- delete segments from dcd file
- delete the most recent atomselect?
- Delete the residue and reassign the residue numbers
- Delete Volume Maps via Script
- Delete water 5 Angstrom away of ligand
- delete water molecules
- Deleting a given bond type by topo tool
- deleting at vmd console
- Deleting atomselect selections for proper memory management
- Deleting bonds based on length
- Deleting frames / molecules does not free up memory!
- Deleting portions of isosurfaces
- deleting specific residues or atoms
- deleting trajectory paths
- Deleting/modifying specific molecule representations
- Delightful repl1ca w4tches at Prest1ge Repl1cas
- Delightsome Cart1er w4tches at Prest1ge Repl1cas
- Delphi binary phi map problem
- dementi: VMD freezes KDE under Linux Redhat = nVidia problem
- Densities for protein and ligand
- density
- Density distribution plots <