VMD-L Mailing List
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About this archive
Starting: Thu Dec 19 1996 - 11:40:41 CST
Ending: Fri Nov 06 2009 - 19:24:04 CST
- ! Obtain degrees from Prestigious non-accredite dUniversities
- "animate readdel"? (was: multiple automated calls to NAMD)
- "cartoon" failing to show secondary structure
- "cartoon" failing to show secondary structure--more info
- "Determine file type" list is far too long...
- "Distributed Cavelib" VMD port
- "Draw" different things in different frames
- "get {x y z}" returns single value
- "Hands-On" Workshop on Computational Biophysics
- "Hands-On" Workshop on Computational Biophysics, July 6-10 and August 10-14, 2009
- "Lines" representation does not show
- "Lines" representation does not show:remote
- "measure fit" inaccuracy?
- "measure fit" problem
- "mol scaleminmax auto" vs. "mol scaleminmax $min_val $max_val"
- "no CUDA accelerator devices available", Nvidia GeForce 9600 GT card
- "Not all atoms have unique coordinates"
- "nucleic" selection
- "pbcwithin" keyword
- "Pick item mode" inactive in OSX bundle ?
- "same as" failing?
- "Save coordinates..." silently overwrites existing files...
- "Selection not understood"
- "Sorry, this version VMD was compiled with Python support disabled"
- "tight" selection
- "truncate_trajectory" a new plugin
- "Unable to create OpenGL window"
- "which files to make a spatial grid?" => Bug for list command?
- # of waters limit
- $64k/yr hpc post-doc@lanl
- 'gopython' Tkinter and Numeric Python error
- '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
- (no subject)
- (UNCLASSIFIED)
- (xterm: Command not found) error
- .cshrc error prevents VMD working on OSX10.3.3??? or something else???
- .grd and .srf
- .pdb file from XMD
- .psf and .params files for IMD
- .psf for porphyrin
- .vmdrc
- .xst file disagrees with pbctools/.dcd file - what are the limitations of pbctools?
- .XYZ File format
- .XYZ File format (DL_POLY conversion)
- .xyz file, namelist index too large error
- .xyz to .dcd using catdcd
- 0ne of a kind repl1cas
- 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)
- 100% of CPU usage
- 15% off on two watches
- 1999 VMD User Survey Report
- 2 more quick questions
- 2 questions
- 20 colors for 20 amino acids!
- 2000 VMD Survey Report is up
- 2006 VMD user survey in progress
- 2D projection
- 3 simple questions from a newbie
- 3-d visualization
- 3D Graphics
- 3D grid data to 2D contour?
- 3D pdf problem
- 3D printing
- 3D visualization
- 3D/stereo hardware recommendations wanted!!!
- 3DConnexion SpaceNavigator in 1.8.7alpha30 on OS X
- 3Dconnexion SpaceTraveler works
- 4x4 trafo matrices to get "homo-two-protein-complex"
- 64 bit NAMD on AIX and CatDCD
- 6DOF controllers
- 99 Toyotas as low as 2% over invoice
- : about complexing protein and ligand!
- <please insert a decent subject here next time, thanks>
- [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
- [Fwd: pdb from trajectory] some clarification
- [Fwd: problems with manipulating control switches on VMS main menu]
- [jrodgers78@gmail.com: outputing secondary structure from timeline]
- [lammps-users] LAMMPS to VMD: lmp2vmd tool
- [lammps-users] MDAnalysis (slightly OT)
- [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
- [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
- [selection problem] When I choose all not 'solvent', one residue is gone?v1.8.3
- [Tech] Colors in VMD
- [Tech] Customizing VMD: hot keys and popup menus
- [VMD TECH] Tracing VMD Variables (Part II)
- [vmd-l] Graduate assistanship in Bioinformatics at NCSA
- [vmd] K3b bug?
- [vmd] max number of molecules on mac
- [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 common list problem
- 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 gas box
- a name quesiton
- 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 question
- a question about "measure fit"
- a question about dcd files
- 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 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 water box containing only the absorbent heads of
- a way to create a nice image
- 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 adding ions to an ion channel pore
- about average structure
- about CHARMM electrostaic potential
- About CHARMM electrostaic potential map
- about CHARMM electrostatic potential
- About Cluster Plug-in
- about command readpdb?
- About drawing bonds.
- about dynamical change color of atoms
- about frame
- about gamess plugin
- about graphics accelaration
- About Hydrogen bond calculation
- about maximum number of atoms
- about measure dihedral angle
- about measuring volume of the binding site
- about new vmd on windows
- About occupancy volume maps
- About openning a file to write in callback function
- about parameter "wrapAll"
- about paratool
- about resid
- about shape order parameter
- about superimposing by VMD
- About Tcl command
- about tcl program and run tcl script in namd
- about the psfgen of vmd
- about TkConsole
- About using trace
- about viewing charge density
- about vmd
- About VMD compile in win32
- about writepdb
- absolute C.O.M motion calculation script: help
- Accelerating your VMD 1.8.7 calculations with an NVIDIA Tesla GPU
- Access to bond information inside a VMD plugin...
- Access to Python libraries from Mandrake8.1
- accessing bonds angles dihedrals etc lists after PSF file is read into VMD
- Accessing TCL through Python interface
- accessing values for selection keywords
- accessing VMD help
- ACE and NH2
- ACTC Triangle Consolidation
- Activation energy
- AD:Family Reunion T Shirts & More
- 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 H-atoms to Pdb file for NMR
- add Mg2+
- Add transparent plane to molecular
- Add transparent plane to molecular structure
- add water on the top of protein border
- Adding a logo to a screenshot
- Adding a Water Box
- Adding Atoms in Colors Menu
- adding atoms to empty molecules
- adding bonds between segments
- Adding bonds in a script
- adding bonds with the mouse and writing psf
- Adding color scale bar on the screen
- adding hydrogen atoms
- Adding labels, etc.
- adding lipid bilayers
- adding new atoms to a molecule from a script
- Adding New Color Definitions to Color Form
- adding residue at start or end
- Adding Salt to a system
- adding selections
- Adding two separate pdb files: Lipid Bilayer's with Protein's
- adding urea to a protein-water system
- adding waters only in top of lipid
- addition on CHARMM electrostatic pot.
- Adjacent surface?
- Adjusting perspective
- Adjusting R/S configuration
- advanced python console
- advanced selections (or explicit pair list) for measure gofr ?
- advice for a PCI video card on redhat
- again :resid of water that is H bonded
- again about average strutcure
- Aggregation analysis
- algorithm for command *within*
- algorithm for finding center of mass of the side chains in the protein
- Alias histidine residue
- Align a PORTION of several structures
- align and superimpose crd structures.
- Align membrane
- Align mistake
- Align protein with different number of aminoacid
- align two molecules with index
- aligning molecules with different number of atoms
- aligning one molecule
- aligning protein based on one helix of protein
- Aligning structures
- alignment
- alignment and rmsd fit
- alignment problem. trying to align new lipid to bilayer, but lipid always has wrong direction?
- Alignment Python
- aligntool
- aligntool docs?...
- All that I never took the time to ask about VMD ...
- all within selection
- Altering Definition of Molecular Coloring Method
- Altering water sphere and charmm type
- alternative display mode of HBonds
- AMBER (old ?) nucleic acids names not recognised
- AMBER parmfiles
- Amber patches for Auto PSF generator
- AMBER pbsa electrostatic potential map
- Amber periodic images
- Amber prmtop/inpcrd files
- amber trajectory
- Amber trajectory loading
- AMBER6 format
- AMBER9 netcdf trajectory loading
- AMD64 vmd installation problems
- amd64/nvidiaFX1100/linux crash
- amidated C-terminus and pyroglutamate
- aminoacid mutation
- An APBS problem
- an arrow for a dipole
- an inconsistance between psf file and coor file after equilibration
- an old...old..old..question
- An remark on PoV output
- analysing big trajectories
- analysing big trajectories (fwd)
- Analysis
- analysis of energy with water excluded from dcd file
- analysis script causes vmd to crash
- analysis scripts: VMD text /batch mode
- Analyzing pdb files remotely with VMD installed locally
- angle between protein domains:
- angle between two vectors
- angles
- Angles and dihedral generation
- ANGLES and DIHEDRALS ... location in VMD code?
- angles and dihedrals in .psf file
- Angles in psf file
- Animate data
- animate delete
- animate error handling
- 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
- animations with molecular surfaces
- ANN: BioCoRE now includes remote job submission
- 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 at Super Computing 99
- Announce: VMD Users Image Gallery
- Announce: ZoomSeq -- sequence browser for VMD
- ANNOUNCEMENT: BioCoRe
- Announcement: QM/MM Workshop
- Announcing MDSalon!
- Another feature request for vmd 1.8
- another trivial question regarding the key setting.
- antialiasing
- Antialiasing ?
- antialiasing problem
- any body else have VMD problems with Linux + ATI FireGL X1-256p + fglrx-glc22-4.3.0-3.7.0
- Any Mac (Intel) users still running 10.4.x???
- Any methods for real stereo viewing with Mac and OsX
- Any way for comparing two structures??
- Any way to output contact map data
- Anyone have catdcd-4.0 for BlueGene?
- Anyone have cyclic structures I can use for testing?
- Anyone using ATI X1600?
- APBS data visualization
- APBS dx colors depend on order of molec files loaded???
- apbs electrostatics
- APBS error
- APBS error : Cannot read output file
- APBS plugin
- APBS Plugin for VMD
- Apologies
- Apologizes for "How to select some sugar atoms"
- Appending to DCD file with "animate write"
- Apple hardware configuration
- Apple VMD not showing gro file properly
- applying 6dof input forces
- applying forces on a protein in VMD
- April promo on w4tches
- Arbitrary values of isosurface
- Archived Spam in the VMD-L Mailing List
- area of protein cross sections
- Area per lipid
- Ask the Cluster Expert
- Assigning Color Codes for stress/force in .xyz trajectory files
- assigning variable names using a for loop
- assigning variables for representations
- assignment of "measure contacts" output to tcl variables
- 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 index number
- atom index starting at 0
- atom name can not exceed four characters in pdb and psf?
- Atom name label
- Atom names, RES-IDS...!!!
- ATOM or HETATM record
- atom position update for reference atom list
- Atom renumbering in DCD file
- atom selection
- Atom selection based on arbitrary columns in the pdb file
- atom serial number
- Atom sorting according to resid
- atom type
- Atom typing
- atom velocity arrows
- AtomLexer/lex.yy.c error
- atoms deleted in patch try to come back
- atoms filter?
- Atoms numbers in VMD
- atoms with changing colors
- AtomSel and Graphics
- AtomSel with object index (Python scripting)
- atomsel: writepdb failed for vmd 1.8.6
- atomselect
- Atomselect in loops
- Atomselect in NAMD GUI
- Atomselect on several molecules
- atomselect protein
- atomselect within
- atomselection
- Atomselection for negative values
- Atomselection in NAMDENERGY
- atomselection in order
- Atomselection problem
- atomselection question
- atomselection: number of residues
- attempting to source a script
- Auto IMD
- auto none /psfgen
- AutoIMD
- AutoIMD and fixedatoms
- autoimd error
- AutoIMD on VMD 1.8.3
- AutoIMD on vmd 1.8.6 IRIX....
- autoimd on windows
- autoionize
- autoionize "error procesing bonds"
- Autoionize / SODIUM
- autoionize behaviour on big systems
- Autoionize plugin
- Autoionize plugin problem
- autoionize plugin..
- autoionize script
- automated loading
- Automatic loading of mol2 files
- Automatic PSF Builder Help
- Automatically shutting down VMD after NAMD terminates IMD connection
- Automatically zoom so that the protein fill the display
- automating graphic representations
- autopfs: unknown atom type error when processing ATP
- Autopsf
- autopsf errors in vmd1.8.5
- autopsf from console
- autoPSF with a POPC membrane
- autostereograms in VMD?
- average area per lipid
- Average coordinates
- Average position of atom set
- Average strcuture
- Average structure
- Average structure and NamdEnergy
- Average Structure and RMSD
- average z-coordinate of a selection
- Averaging volmaps
- avoiding distance based bond search when reading a PDB file
- AW: volumetric maps
- Away from email until Sunday...
- Away from VMD-L/email until July 8th...
- Away until July 12, self-help encouraged!
- Axes
- Axes are not rotated?
- Axes dilema
- B factor calculation
- B-factor Plot
- Babel and VMD
- Babel and Windows
- babel compilation error
- backbone dihedral angles over trajectory
- Backbone representation of RNA
- Background colour
- Backspace and delete
- Backspace not functionning in console
- bad angels
- bad angels]
- Bad performance of VMD
- bad resolution and too slow on mandrake 10.0
- badwater script - help
- base plane not being filled in for terminal adenines in ribbons/new ribbons
- Basic membrane plugin questions
- Basic VMD questions...
- Batch mode on Mac OS 10.5.3
- batchmode use of "labels" functions?
- 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
- Best fit plane axis
- Best hardware for 3d.
- Beta color of atoms
- beta column format in PDB
- beta version
- Big trr trajectory
- bigdcd
- Bigdcd - get coordinates from file
- bigdcd v2.0 testers needed...
- bigdcd v3 available. testers needed.
- bilayer thickness in simulation of POPC membranes
- 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?
- BMP snapshot
- bond connectivity for different frames
- bond connectivity not displayed in VMD
- BOND CP2 - CT2 IN PARAMETER FILES
- Bond display and Periodic Boxes
- bond distance across different proteins
- Bond drawing questino
- Bond in pbc condition
- Bond information
- bond information in psf file
- bond length
- bond length definition
- Bond Lengths
- Bond lengths from PDB and PSF
- bond missimg
- Bond representation of coarse grained molecules
- bonding across periodic boundary
- Bondlength information!
- bonds across periodic boundaries
- bonds forming during simulation
- bonds in .psf file
- bonds in graphical representation
- bonds not created as desired
- boolean operators in graphics
- boubt about consistency of measures
- Boundry Dimensions for Solvation
- Box dimensions
- box information
- box information amber crdbox
- Box of non-polar solvent
- 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
- Broken tube drawing method?
- bug in comments interpretation of vmd
- 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-1.6 (linux, GL)
- bug report in VMD 1.8.5
- BUG with MODEL card in PDB file
- bug?
- Bugfix: new save_state.tcl for VMD 1.8 installations...
- Bugs ? Representation window does not update new material
- Build a VMD forum?
- Building a sphere of atoms around a chosen atom
- building an uncoming sulfide bridge
- building bilayer with DOPC or other lipids
- building loops
- Building LPS membrane
- Building plugins with Borland Bcc32
- Building polymer psf from monomer topology
- building psf with CMAP, old topology remark entries still in psf
- Building VMD in Windows
- building VMD on LINUX
- building VMD on SGI IRIX 6.x
- Building VMD on windows 2000
- Building VMD under Windows 2000
- Buried Surface Area
- C NH1 C minimization error
- ca contact map
- CA-CA distances in a trayectory
- Ca-dist script
- caculate the RMSD of 10 DNA
- Calculate accessible surface area
- calculate charges of the binding site residues with psfgen
- Calculate density
- Calculate End-End distance for DCD
- Calculate Free Volume?
- calculate rmsd in a loop:feedback [sorry if you get it twice]
- Calculate the area of overlap?
- 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 changes
- Calculating dipole moment of protein
- calculating distance between center of geometry/mass of methyl hydrogens for all residue pairs
- calculating lipid order parameters
- Calculating minimal distance between two groups
- Calculating pocket volume
- 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 volumes enclosed by SAS
- Calculating volumetric data for a molecule
- calculation limit of gofr?
- calculation of alpha helical content
- calculation of free energy between lipid membrane and protein
- calculation of RMS values
- Calculation of RMSF
- Call to Stride program failed
- Calling Python hackers....
- calling scripts from the command line
- Camera in VMD!!!
- Can a script change the projection?
- Can any of you help me out in building VMD pls
- Can anyone help me out with this script
- Can bonds radius be controlled by tcl command?
- Can I build a structure by VMD?
- can I combine several dcd files into one dcd file?
- Can not enter text in VMD plugin window
- 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 display a box?
- Can vmd do symmetry operation?
- 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 fix the position of two atoms while minimization?
- Can we get secondary structure from PDB files?
- Can you show me an example of the .xyz file that is used to calculate the IR spectrum
- can't add packages
- Can't compile VMD 1.8.3: Tachyon 0.97 needed
- Can't execvp vmd_SOLARISX86
- Can't import python math module
- Can't load a large dcd?
- can't read pdb file
- can't see all frames in XYZ file
- Cannot load file for SASA analysis
- Cannot load Gromos96 trajectory file (attached)
- Cannot perform RMSD analysis
- Cannot read MSMS facet file
- Cannot run IED! :(
- Cannot start CAVE display
- capturing box dimensions from amber coordinate files
- Card for VMD with OpenGL & Linux
- carnal output trajectory
- cartoon problems (encore)
- cartoon representation
- Cartoon representation for large molecules
- cartoon representation of 1crn
- cartoon selection
- Catching error info before it shuts down ...
- catdcd
- catDCD 4.0 and xplor
- CatDCD Desmond Support
- catdcd in Windows
- CatDCD Question
- catdcd vs readdcd.h error checking
- catDCD- convert DCD format
- catdcd.LINUX
- Catdcd?
- cave
- CAVE & Vmd
- 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
- CDROM/Windows/Linux
- center command
- center of mass
- center of mass position
- center scaling and rotation
- center selection problem
- Centering GPCR onto Lipid Bilayer
- Centering of the view on one atom
- centering seection on screen
- centering selection on screen
- centering the molecule
- Centre of gravity for movies
- CG bead definition
- CG Map Tool Syntax Error
- CGTools error: atom select: cannot parse selection text...
- CGTools Plugin
- chain fails
- change axes name
- change color from script
- change cylinder surface properties
- change default bond cutoff distance
- change default drawing and coloring method
- change location of temporay file storage (Win2k
- change location of temporay file storage (Win2k)
- Change properties of representations - batch mode
- Change representation default from lines to points
- Change requested in lammps plugin for VMD
- 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
- Changing a structure of macromolecule with VMD
- changing atom number in animation
- Changing atom order in DCD structures?
- Changing Beta values for each frame of a trajectory..
- changing bond color
- changing certain dihedral angles while keeping rest of molecule fixed
- Changing color of a given atom
- Changing colors
- changing colours isosurface
- changing cpk shere scale in TCL
- 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 frame
- Changing Graphical Representations
- changing occupancy for bunch of PDB file
- Changing Text Style
- Changing the atom species during animation
- 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 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
- Charge coloring and Stereo hot keys
- Charge State Confusion
- charge surface area
- Charlie Buy your loved one Hermes
- Charm force field for POPS lipid
- charm27 forcefield_topology
- charmm binary ele. pot.
- CHARMM CRD files: COR plugin
- CHARMM electrostatic potential
- Charmm expanded coordinate file format?
- CHARMM TO AMBER FORMAT CONVERT
- CHARMM to AMBER trajectory conversion
- charmm toppology : internal coordinates
- charmm vs amber
- Cheap 3D Glasses
- chime vs vmd
- chloroform box
- Chloroform Solvent Box
- Choice of a Linux machine for VMD and high-end computing
- Chromium
- Cionize on mac cuda
- Cl ions
- clarification to "problem using pbc wrap"
- classify and compute the forces between two atoms
- Classroom Stereo projection
- Clip
- Clipping plane tool and export
- clipplane
- cloning a molecule
- closewater.tcl
- Closing filehandles in vmd tcl script
- Cluster analysis
- Cluster Analysis given a dcd trajectory
- Cluster plugin and Gromacs g_cluster
- clusters visualization with colours
- CMAP and psfgen
- CMAP problem
- CMYK
- CMYK images
- cns files
- CNT Analysis
- colomb map in volmap tool
- Color a protein based on a property
- Color bar
- Color bar in VMD
- color by charge (can colors be changed?)
- color by frame?
- color by resid
- Color by volume
- Color by Volume on an Intel 945GM
- Color code
- Color error on loading
- Color of bond betwen atoms with different colors
- color problem with Ati Fire GL E1
- Color problem.
- color protein based on an event during a trajectory
- Color Scale Data Range
- Color surfaces by electrostatic potential
- color the surface with electrostatic potential value
- color update for xyz trajectory
- color: negative values
- colorid
- coloring according to charge of residues
- Coloring atoms by a general scalar
- Coloring based on POS
- coloring by atom type
- Coloring by BETA not updating per frame
- coloring by charge
- Coloring by type?
- coloring HIE, HIP, HID: sorry ... I got it
- coloring method
- coloring method User
- coloring method)
- coloring method: user
- Coloring mols by carbon only
- coloring names
- coloring of an item created by canvas
- Coloring of atoms/molecules
- coloring of trajectory
- coloring residues with VMD
- 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
- colors
- colors changed in animation
- colour residues
- Colouring
- Colouring Atoms according to the centro-symmetric parameter
- Combine Drawing Methods - Cartoon and Disulfide Bonds
- combine together two PBD/PSF files
- combine.tcl
- combine.tcl error
- combine.tcl membrane plugin
- command args to MSMS in VMD
- Command line argument
- command line dcd to trr?
- Command line troubles
- Command to change background to gradient
- Compilation
- compilation error
- compilation from source: first attempt failed
- compilation from source: make error message
- Compilation issues with tcl.h
- 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 a plugin source code
- compile catdcd.c
- Compile from Source Crashes 5/11/04
- Compile of OpenGL shader vmdsphere failed
- compile problem for VMD1.8.6: OpenGLRenderer.C
- compile VMD on freebsd 4.8
- Compiled version for MacOSX with non-standard options
- Compiling CATDCD and VMD plugins on AIX5.2
- Compiling from source on Mac OS X 10.5
- Compiling NAMD from SRC: Tungsten@NCSA
- Compiling problem
- compiling problems
- Compiling VMD
- compiling VMD 1.8.3
- Compiling vmd for ppc linux
- 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 under Windows XP
- Compiling VMD with full OpenGL
- Compiling VMD-1.8 as a loadable python module
- compiling vmd...
- Compiling VMD: Trouble with DispCmds.C
- compiling/porting vmd
- complete residues within
- compose pdb
- Compressed files
- compressed trajectory support
- 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
- Computing angles
- concatenate protein and 2 ligand 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(???)
- configuring vmd w/ browser on OS X
- conformational alignment
- conformations of a linker
- Connecting a phantom with NAMD and VMD
- Connectivity lost when loading second pdb
- connectivity problem
- Consider fluctuating volume for density
- console in vmd-1.8.3 amd64 is blank (like white text on white background) so I can't see any output messages
- constant region selection for animation
- constraints
- contact between 2 residues
- contact map
- contact map (over all frames)
- contact map definition
- contact map lig-pro
- contactmap for RNA
- contour plots
- Contribution of selected atoms to surface
- control drawing method
- Control of aminoacid ionization in VMD
- Conversion of trajectory files
- Convert an ascii matrix to an image
- convert DCD files to GROMACS .XTC format
- convert PDB file to CRD?
- convert pdb to psf
- convert tcl to python
- convert THR and SER to the phosphorylated forms
- converting
- Converting .txt trajectory files to VMD compatible format
- Converting Files with VMD
- Converting graphics to a pdb's coord system
- converting pdb to xtc
- converting trajectory files with catdcd in command line
- convex hull and VMD
- coordinate translation
- coordinates of an atom
- coordinates with get command
- CoordinateTransformation
- Copying a selection
- copying parts of an atomselect selection
- 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
- Correlated motion
- correlation
- Correlation Functions
- corrigendum: error when solvating a system
- Corrupt cpmd-vmd.pdf File?
- Could not locate 'dowser' (Program not found message box)
- could not make avi file
- could not visualize DCD file downloaded from VMD website
- couldn't fork child process: not enough memory
- couldn't open "c:/multiseq-406080740227.start.domain": invalid argument
- Couldn't open required GL library
- count variable number of molecules
- counting gas molecules inside the nanotube
- Counting H-bonds from a dcd file
- Counting number of hydrogen bonds in the representation
- counting selected atoms---selection time series
- covalently bonded atoms
- CPK Graphical Representation
- crash on ubuntu linux
- CRD problems and CRD to DCD conversion
- Create a new color category
- Create a PSF
- Create atom selection from list of integers
- create movie from multiple frames
- create new colors
- create new topology file for new molecule
- create new topology file for new molecule]
- create psf and dcd from pdb
- Creating a cuboid box to fit in atoms
- Creating a demo - updating the OpenGL window
- Creating a VMD movie from a Tcl script
- Creating bond between two atoms
- creating gif animation with povray
- creating movie files
- creating nonstandard solvent
- creating periodic images of an atom
- creating psf from pgn
- creating psf with trimethoprim
- creating scripts
- creating spherical water droplet
- creating videos where the representation changes throughout
- criteria for detecting hydrogen bonds
- cross correlation in VMD
- 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 an a cluster ?
- CUDA Support
- Curious about analytical capabilities of VMD
- cursor size/shape in pick mode
- custom db in Multiseq
- Customized radii
- Customizing vdw radius
- Customizing VMD Sessions
- cutting short a DMPC bilayer in VMD
- CVS access is back online...
- cvs plugins do not compile because of errors in the sgsmooth.C
- CVS root directory not found
- cylindrical water
- Cylindrical water box
- Data fields in vmd
- data file extensions
- DCD architecture dependence
- DCD command-line options
- DCD file
- 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 large files, charmm-VMD
- dcd reading error
- dcd reading routines
- dcd to coor files
- DCD to XYZ conversion)
- dcd tools
- DCD unit cell data
- dcd with fixed atoms
- debug
- debugging tool for atomselect
- default colors
- default directory
- Default parameters for image renderers
- Default radii and colors
- Default resource file (.vmdrc)
- defining bonds
- Defining Bonds in .xyz file format
- Defining graphics colors
- defintion of alpha helix in vmd?
- delatom "no segment..."
- delatom usage - no such segment?
- delete bonds in TIP3P
- delete bonds in TIP3P water model
- Delete frames in a script
- Delete overlapping residues
- delete residues from trajectory
- Delete Volume Maps via Script
- 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 specific residues or atoms
- 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
- density profile
- density profiles
- deposition simulation from lammps
- Depth Cueing and dispdev none
- Desmond trajectory conversion to dcd format
- Details of .psf format
- determining vdw, elec, and others
- developing plugins to vmd in python
- Dialboxes
- dict command
- difference for solvating a protein in long box suing or not using Molecule Dimensions
- different colors
- different number of atoms in different frames of a trajectory
- Different number of atoms trajectory frames
- different numbers of frames even though...
- differentiating solvent molecules......
- difficulties referencing a variable within a namespace
- Difficulties using Crystal Eyes 3
- difficulties with starting vmd
- difficulties with starting vmd (fwd)
- difficulty in installing VMD on linux.
- diffusion coefficient
- diffusion coefficient from rmsd
- Diffusion Constant
- digest form
- DIHE in topology file
- dihedral & g(r)
- Dihedral angle calculation!
- Dihedral angle calculations for alanine dipeptide
- dihedral angles
- dihedral angles at the ends
- dihedral angles cleaned up
- dihedral angles cleaned up!
- dihedral angles for a lot of identical molecules
- Dihedrale angles in VMD
- diplaying multiple frames from DCD file
- dipole
- dipole moment
- dipole moment - corrigendum!
- Dipole moment?
- Direct manipulation of the camera
- Disable the set output
- Discrepancy between colours when coloured by timestep and Tachyon rendered
- discriminate aromatic ring face
- display all frames simultaneously
- Display alternative atom locations using vmd
- Display bond between fragment and protein residue
- Display bond breaking
- display bonds
- display Gaussian cube file
- Display Grasp potential map in VMD
- display hexagonal periodic system
- Display issue on VMD for Linux
- Display not updated when using move() from Python in VMD 1.8.6
- display of electron density maps
- Display of H-bonded waters only
- display of periodic DCD information
- display of periodic DCD information/PBCTOOL
- Display on a Graphic Cluster
- Display only side chains
- display panel only showed 1/4 of its area on the screen.
- Display problem
- Display shuts down on startup
- Display size in VMD 1.8a29 for OS X
- Display the electrostatic character (delphimap) on the structure file
- Displaying biological unit revisited
- Displaying Counter alongside animation
- displaying double, triple bonds
- displaying hydrogen bonds when hydrogens are not available
- Displaying local water molecules throughout trajectory
- displaying many frames with periodic images
- Displaying nearest images using PBCTools
- displaying neighboring residues
- displaying residues within 5 A of ligand in vmd
- Displaying simulations and rotations
- Displaying the periodic box ...
- displaying tube/ribbon with varying diameter ?
- displaying velocity from dlpoly history
- Distance between COM for 2 chains for each frame of trajectory
- Distance calculation in TkConsole
- Distance measurement via measure bond
- distance of two center of mass
- distance to solvent accessible surface
- distance tween two atoms
- Distance, angle
- distances
- distances on a isosurface plot
- distribution analysis
- Disulfide bonds
- Disulfude bonds
- disulphide bond
- disulphide bond formation
- Divide by Zero Error , but can't find the zero!
- DL_POLY output files
- dll by c++ cannot be recognized by VMD tk console ?
- DLP Stereo and VR toolkit integration with vmd
- DLPOLY HISTORY FILE in VMD
- dlpoly history files in vmd 1.8.4
- dmpc membrane
- DNA and low pH
- do not compute/draw bonds?
- Dobule and triple bonds
- docking
- docking in VMD
- Does command "animate delete all" free memory?
- Does VMD support cfg file format?
- Does Vmd support GUI and rendering separate
- Does VMD support LES simulations?
- Does VMD support LES simulations?]
- Does VMD support to draw a velocity field diagram?
- Does volume coloring require GLSL rendering?
- dots per inch?
- double bonds
- double image for one eye with crystal eyes stereo
- doubling a membrane
- doubts in movie making using vmd.
- download pdb files from PDB with vmd 1.8.4b10
- Download the newest version of VMD
- Download vmd for 64-bit Intel Itanium
- Downloadable version
- DOWSER: child process exited abnormally
- DPPC Bilayer Size
- Draw a circle
- draw a vector
- Draw Bonds
- draw command
- draw command with different material
- draw hydrophobic contact
- Draw in a new layer problems
- draw line
- draw lines
- draw multiple frames
- draw text or title in pov
- Drawing a line between two atoms
- drawing a membrane
- drawing a plane
- drawing a truncated octahedron
- Drawing atom - atom bonds
- drawing bond for coarse grained model
- drawing bonds
- Drawing bonds to metals
- drawing bonds with vmd/python interface
- Drawing electron density surfaces (from cube files)
- drawing helices from partial aminoacids
- drawing lines
- drawing objects
- Drawing of bonds while trajectory animation.
- drawing of direction vectors for conformational transition
- Drawing oriented cylinders
- drawing poligons
- drawing spheres
- drawing the edges of a non-rectangular box
- drawing trajectory of a molecule
- Drawing Vectors
- drawing waterbox
- dssp in vmd
- dssp in vmd (II)
- dti monitor linux
- dublicated residue name in PDB/PSF
- dumb movie maker question
- dummy atom ?
- dummy atoms and FEP
- duplicate atom coordinates in PDB files
- Duplicate VMD-L emails...
- duration of video mpeg
- Dynamic 'Determine file type' list in main menu !?!
- Dynamic bond calculation
- dynamic bonding
- Dynamic bonds and H2 molecules.
- dynamic bonds question??
- dynamic coloring
- Dynamic selection of residues in a trajectory
- Dynamic selection of residues on a trajectory
- dynamical list of atoms
- dynamically changing label...
- DynamicBonds representation
- E-D stereo glasses
- easy way to adjust dihedral angles?
- ed and vmd
- eigen values
- Eigen values of Moment of Intertia Tensor
- EIGENVECTOR ANALYSIS
- Elastic Properties
- electric field
- Electron density
- Electron Density Map Display
- electron density map is shifted?
- Electron density profile
- Electron microscopy surface with VMD?
- Electrostatic - PMEpot
- electrostatic energy
- electrostatic map render problem
- electrostatic potential
- Electrostatic potential mapping
- electrostatic potential maps in vmd
- element Si
- eliminate atoms from psf and pdb files
- Elliptic molecules
- embed VMD in web page
- Empty Extension menu on OSX
- enable direct rendering DRI on fedora core 2
- Enabling a menu on the top level
- enantiomers
- Energy
- energy calculation in VMD
- energy minimization of a trajectory with vmd+namd
- Energy plot script
- entropy calculations
- equilibrating a membrane patch
- Equivalent Mouse Capabilities to Tracker CAVELib
- Erro compiling vmd and or fltk
- error - with unknown atom type +CA
- error after changing of PYTHONPATH variable
- error Autoimd
- Error compiling trio
- error during creat .psf file
- Error Encountered in making vmdmovie
- Error generating psf files
- Error in "measure fit"
- Error in changing on screen options of VMD
- Error in Linux
- error in loading psf file generated from lammps data file.
- Error in modifying and concatenating two pdb files into one [plz Help!]
- error in psfgen file
- Error in running VMD on AMD64-bit machine (Fedora Core 4)
- Error in visualizing the 5 prime end of DNA strand
- Error installing VMD 1.8.5.
- Error loading .cor files from CHARMM using dcd
- error loading dcd file on Windows XP
- error loading pdb files
- Error message disappears before I can read it!
- error message from IED
- Error message in VMD console when I try to switch to Python mode.