Frequently asked questions about VMD (2022)

Table of Contents
Frequently asked questions about VMD Documentation What documentation is available for VMD? General information Where is the best place to find out about VMD? How do I reference VMD in publications? Is there a VMD mailing list I can subscribe to? Do I need NAMD to run VMD? Hardware and Software Installation What platforms is VMD available for? I have problems downloading VMD from your web site. What can I do? How do I install VMD? When I try to compile VMD I get error messages; what should I do? Features Can VMD load PDB files containing more than 99,999 atoms? Does VMD have any molecular editing features? How can I add extra graphics to VMD What file formats does VMD support? Can VMD show orbitals, electron densities, normal mode vibrations,etc. on the screen? Why doesn't VMD have feature X? But I really need feature X! What can I do to help develop VMD? Use Using the atom selection commands, is it possible to select onlythose atoms which are within a specified distance of (a) a specifiedatom (b) a specified location in space? Is there a faster way to change the rotation/translation/scalemode than using the mouse menus? Does VMD have any hot keys for changing the mode? How do I connect the bonds correctly when I don't use a PSF file? Why doesn't VMD read the CONECT records from the PDB file? Why does VMD sometimes add an extra bond between the hydrogens ofwater molecules when I read in both a PDB and a PSF file. How do I display molecular dynamics trajectories with VMD? My molecular trajectories are not in DCD/CRD format. Can I still use VMD to visualize them? Can one view electrostatic distributions with VMD? Can I edit the secondary structure results found by STRIDE? Is it possible to perform rotations about an object other thanthe center of VMD's bounding box? Is it possible to select two atoms, draw a dotted line between them,but don't display the distance? Is is possible to modify the depthcue slope in VMD? FAQs Videos

Frequently asked questions about VMD

Documentation

What documentation is available for VMD?

Quick help, this FAQ, User's Guide, Installation Guide, and Programmer's Guide are available in various PDF, Postscript, and HTML versionsHere.

General information

Where is the best place to find out about VMD?

The VMD home page, located at http://www.ks.uiuc.edu/Research/vmd/.

How do I reference VMD in publications?

Suggested citation text and a Bibtex entries are available here

Is there a VMD mailing list I can subscribe to?

See the VMD-L mailing list page for more details.

Do I need NAMD to run VMD?

No, you do not need NAMD just to use VMD as a visualization program. You only need both programs if you plan on running linkedinteractive molecular dynamics (IMD) simulations. See the NAMD home page for more information about its features.

Hardware and Software Installation

What platforms is VMD available for?

We have compiled and tested the OpenGL version of VMD on AIX 4.3, Linux, MacOS X, IRIX 6.x, HP-UX 11.x, Solaris 7/8/9, Tru64 Unix 4.0F, and Microsoft Windows 2000/XP. Binaries for these platforms are available from the WWW site.

I have problems downloading VMD from your web site. What can I do?

Please try again, preferably during off-peak hours. If you continue to have problems, send mail to vmd@ks.uiuc.edu describing yourdilemma and we'll help you resolve the problem.

(Video) VMD

How do I install VMD?

Read the installation manual.Precompiled versions are available for all major platforms andare very easy to install.

When I try to compile VMD I get error messages; what should I do?

If you're compiling from source, make sure to check theVMD programmer's guidefor FAQs and suggestions.

Features

Can VMD load PDB files containing more than 99,999 atoms?

Yes. VMD can load a properly formatted PDB file with an arbitrarynumber of atoms. VMD is able to do this because it ignores the atomindices stored the PDB file itself and instead it uses its own internalnumbering scheme. As long as your PDB file follows the strict column rulesfrom the PDB spec, VMD doesn't care how many atoms are in the file.

Does VMD have any molecular editing features?

You can use VMD to move atoms, residues and fragmentsaround via the "Mouse" menu.

The text user interface will let you manipulate the atom coordinatesin almost any fashion. See the user guidefor more information on how to write scripts. It can also be usedto change the beta and occupancy information.

If you want to build/edit structures beyond what is described above,you'll need to use the psfgen plugin for this purpose.

How can I add extra graphics to VMD

There are two major ways of doing this:

(Video) The HD-VMD Conclusion - Uncovering the real stats behind this failed format

  • One way is through a Raster3D, GRASP, or STL input file. VMD can read and display the contents of these files (with some limitations) which you can manipulate as it were another molecule.
  • The more general solution is to use the "draw" and "graphics" text commands in VMD. With this you may add objects like lines, cylinders, triangles, text labels, and more, completely inside VMD.

What file formats does VMD support?

Supported file formats are listed with the other VMD plugins.In addition, VMD can use Babel to convert other formats automaticallyinto the PDB format then read those files.

Can VMD show orbitals, electron densities, normal mode vibrations,etc. on the screen?

Yes. VMD now supports many of the common density file formats, andcan display isosurfaces, slices, and texture other representationsby this data.

Why doesn't VMD have feature X?

Because we either haven't thought of it, haven't needed it, or haven't had time for it yet. Send us a suggestion!

But I really need feature X!

VMD is written in C++ and has documented source code(see the Programmer's Guide).You can probably add features or make minor modifications yourself.

What can I do to help develop VMD?

There are many things we would love to do with VMD but haven'thad the time. Here's a short list of things, but many more things arepossible:

  • Develop useful scripts for the script library
  • Write tutorial scripts that can be used over the web
  • Make pretty images with VMD for our image gallery
  • Make useful suggestions and point out bugs.

Use

Using the atom selection commands, is it possible to select onlythose atoms which are within a specified distance of (a) a specifiedatom (b) a specified location in space?

The first one is easy, try an expression like 'within 5 of protein'.This selects all atoms within 5Å of all the protein atoms(including the protein atoms themselves). The second one is morecomplicated. The way to do that is to specify something like'sqr(x-3)+sqr(y-4)+sqr(z+5) < sqr(2)' which will select all theatoms within 2Å of the point (x,y,z)=(3,4,-5). We may somedayadd the selection 'within distance of point x y z tosimplify this very common selection.

Is there a faster way to change the rotation/translation/scalemode than using the mouse menus?

-or-

(Video) Hydrogen bonding analysis of protein dynamics in VMD

Does VMD have any hot keys for changing the mode?

Yes, look in the section of the manual describing the hot keys.By default, 'r' changes to rotation, 't' to translation, and 's'to scaling. Press 'c' to center on a given atom. There is evena text command, "user add key <character> <script command>"which sets character as the hot key for the given command.

How do I connect the bonds correctly when I don't use a PSF file?

-or-

Why doesn't VMD read the CONECT records from the PDB file?

VMD uses one of two ways to find which atoms are bonded. If both aPSF and PDB are given, then the bond records of the PSF are used. Ifa PSF is not given, then the bonds are determined from a distancesearch, but if the unbonded atoms are too close (this usually occurs with modelbuilding) they will be connected as well.

The usual way to fix this is to include CONECT records in the PDBfile. Since we don't use this feature and have no programs thatreally need it, we don't have anything in VMD to read those records.We realize that not everyone has X-PLOR so we've included a programwhich will convert the CONECT records to a PSF file. It is called'conect2psf' and is located on our web site at http://www.ks.uiuc.edu/Development/MDTools/conect2psf/.Only a binary for SGIs running IRIX 5.x is available.

Why does VMD sometimes add an extra bond between the hydrogens ofwater molecules when I read in both a PDB and a PSF file.

This happens most often when the PDB and PSF records are written fromCHARMm. The water model used for CHARMm adds an extra bond betweenthe two hydrogens. Thus, the PSF has a bond in it so VMD displays it.It isn't possible in VMD to add or remove bonds. However, it is possible,though somewhat cumbersome, to not display them. Here is the way to doit: Suppose the water oxygens have the name O and the hydrogens areH1 and H2. Then you should make two views in your desired representation.In one view select 'water and name O H1' and in the other view select'water and name O H2'. This hack will work, but it means that everytimeyou want to change one (for instance, changing the coloring method) youwill have to change the other as well.

How do I display molecular dynamics trajectories with VMD?

VMD can read molecular trajectories from XPlor/CHARMm DCD files, AmberCRD files, a set of PDB files, or from a running molecular dynamicsprogram. If your dynamics output is already in DCD format, then withthe "Mol" form, choose "Load Molecule" to directly load this DCD filealong with its corresponding PSF or PDB specification. A similaroption is available for reading an Amber structure along with its CRDfile.

The "Animate" form can then be used to playback the simulation. Ifyou have a collection of PDB files, or a hybrid set of PDB and DCDfiles, then you will want to open the "Edit Animation" form. With thismenu you can read in new coordinates to be appended to the end of thestored animation list for a selected molecule. This same form can beused to write out parts of the animation in DCD, CRD or PDB format.This is a useful option for merging trajectory files or exportingsingle frames of a given simulation. Please see the VMD User's Guidefor detailed instructions regarding these menus. You will also wantto consult the User's Guide if you plan to display trajectoriesdirectly from a simulation program such as NAMD.

(Video) vmd Potential Interview clip

My molecular trajectories are not in DCD/CRD format. Can I still use VMD to visualize them?

Tricky question. Some file formats, like XYZ, can contain animationcoordinates. VMD calls Babel to convert the XYZ file into a set ofPDB files, and then it reads in each PDB file. So for the fileformats supported by Babel, the answer is yes. You could similarlywrite your own code to convert your format to a series of PDB filesand read them in by hand (or with an automated script). Thirdly,you can use the "animate dup" command and write your own reader, butI wouldn't suggest this to any but experienced Tcl programmers.

Can one view electrostatic distributions with VMD?

The answer is a qualified "no."It is possible for one to color atoms by atomic charge, but VMD presentlyhas no facility for generating electrostatic potential surfacescorresponding to a set of molecular coordinates.

Can I edit the secondary structure results found by STRIDE?

Yes, you can, with the VMD command "structure" which is accessiblethrough the scripting interface. The "structure" command takes the following parameters: molecule id, atom selection, structuretype. For example, possible structure commands include

structure 2 {resid 10 to 38} helixstructure top {chain B} beta_sheet

The available structure types are:

  • helix = alpha_helix
  • helix_3_10
  • pi_helix
  • sheet = beta_sheet = extended_beta
  • bridge_beta
  • turn
  • coil

For more information regarding the scripting interface, consult theUser's Guide.One warning: The graphics do not update automatically whenthe secondary structure definitions change. If you change thedefinitions you will have to "update" the graphics for that molecule.This will be fixed in a future version of VMD.

Is it possible to perform rotations about an object other thanthe center of VMD's bounding box?

Yes, you can place the center at the location of any atom. With the right mouse button, click on an atom that youwould like to rotate about. This will bring up a menu with severaloptions, one of which is "Pick Item.". Drag down to this selectionand then choose the "Center" choice which appears. The center isthen at the location of the atom.

Is it possible to select two atoms, draw a dotted line between them,but don't display the distance?

Not directly. However, this capability is available through thescripting interface. For instance, suppose the two atoms to connect are "resid 45 and name CA" and "resid 99 and name N".Then the following script will do what you want.

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# make the two selectionsset sel1 [atomselect top "resid 45 and name CA"]set sel2 [atomselect top "resid 99 and name N"]# get the coordinateslassign [$sel1 get {x y z}] pos1lassign [$sel2 get {x y z}] pos2# draw a white line between the two atomsdraw color whitedraw line $pos1 $pos2 style dotted width 2

To understand this information, see the sections in the VMD manual regarding the scripting language.

Is is possible to modify the depthcue slope in VMD?

Not at the present time.

FAQs

What can VMD do? ›

VMD is designed for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure.

How do I open a XYZ file in VMD? ›

xyz. You can load this file into VMD by just typing vmd al-h2o_6.

How do I exit VMD? ›

exit: Quit VMD.
...
The log file may be played back later by using the play command.
  1. console: Log commands to the VMD text console.
  2. filename : Turn on logging to filename .
  3. off: Turn off logging.

What file type does VMD use? ›

VMD natively understands six molecular data file formats: PDB coordinate files, CHARMM and X-PLOR style PSF (topology) files, CHARMM and X-PLOR style DCD trajectory files, Amber structure and trajectory files (i.e. PARM and CRD), and Gromacs (i.e. GRO, G96, XTC, TRR) structure and trajectory files.

What files can VMD read? ›

VMD natively understands several popular molecular data file formats: PDB coordinate files, CHARMM, NAMD, and X-PLOR style PSF topology files, CHARMM, NAMD, and X-PLOR style DCD trajectory files, NAMD binary restart (coordinate) files, AMBER structure (PARM) and trajectory (CRD) files including both the old format and ...

How do you select atoms in VMD? ›

As with many molecular graphics programs, an atom can be picked by moving the cursor over it and clicking the left mouse button.

How do I change directory in VMD? ›

You can open the tkcon window and use the cd command to change directory. each space with a backslash.

How do I change a VMD file? ›

After a few seconds, you can download VMD files. 🔻 How do i change VMD to another format? Upload your VMD-file on the page. Select target format and click "Convert".

What is CPK in VMD? ›

`CPK' is a combination of both `Bonds' and `VDW' in that it draws the atoms as spheres and the bonds as cylinders. The resolution and radius can be modified independently. The radius of the sphere drawn in CPK mode is by default smaller than the sphere drawn in VDW mode, but this radius can be made larger.

How do I import files into VMD? ›

How to load a pdb structure in VMD ? - YouTube

How do I view a VMD file? ›

Windows: Select Start -> Programs -> VMD. Upon opening VMD opens three windows (Figure 1): the Main, OpenGL Display and Console (or Terminal on OS X) windows. To end a VMD session, go to the Main window, and choose File -> Quit. You can also quit VMD by closing the Console or Main window.

Is VMD a software? ›

VMD is molecular visualization software for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.

Is VMD software free? ›

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS X, Unix, or Windows, is distributed free of charge, and includes source code.

Is VMD open source? ›

An open-source application for modeling, visualization, and analysis of biomolecule systems such as proteins, nuclear acids, and lipid bilayers.

How do I take a picture in VMD? ›

To use the snapshot feature, simply open the Render and choose the snapshot option. VMD will automatically capture the contents of the graphics window, and attempt to save the resulting image to the requested filename given in the Render form..

How do I zoom in VMD? ›

The Scale mode will allow you to zoom in or out by moving the mouse horizontally while holding the first (left) button down. It should be noted that the previous actions performed with the mouse do not change the actual coordinates of the molecule atoms.

How do you remove labels in VMD? ›

A label can be turned on or off without deleting it, by selecting the label in the central browser and pressing the Hide button. To turn it back on, select it again then press the Show button. Press the Delete button to delete it.

How does VMD measure distance? ›

Distance Measurements in VMD - YouTube

How do you move molecules in VMD? ›

To move the molecule towards or away from you, hold the middle button down and move the mouse right or left, respectively. Pressing either the left or middle button down and moving to the right enlarges the molecules, and moving the mouse left shrinks them.

What is all atom MD simulation? ›

All-atom molecular dynamics (MD) simulations enable the study of biological systems at atomic detail, complement the understanding gained from experiment, and can also motivate experimental techniques to further examine a given biological process.

How do I open a VMD file in Terminal? ›

Once VMD is installed, to start VMD: Mac OS X: Double click on the VMD application icon in the Applications directory. Linux and SUN: Type vmd in a terminal window. Windows: Select Start → Programs → VMD.

How do I change the color of atoms in VMD? ›

It involves going to: Graphics --> Colors; then within the Categories list on the left of the panel are three choices (Name, Type, Element). Each of those allows you to assign C (carbon) a specific color. This is useful if you want the bonds between atoms to be half one color and half another (e.g. C - N).

What is NAMD and VMD? ›

NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PLOR.

How do you align structures in VMD? ›

Click the Align button. Right-click on the structure you aligned (the one that is NOT the reference) in the VMD Main window, and select Save Coordinates… to save your new aligned structure to a new file.

How do I delete a box in VMD? ›

Save your visualization state as vmd file. Then, open the file using text editor, delete the box section.

How do I save a VMD session? ›

There are two ways to do this in VMD: In the main menu, press the Save State button found in the File menu; this will bring up a browser window where you can enter a file name in which to save your work. In the text console, type save_state filename, where filename is the name of the file in which to save your work.

Which is better VMD or DVM? ›

A VMD is the exact same degree as Doctor of Veterinary Medicine; however, the letters “VMD” stand for the Latin terminology, Veterinariae Medicinae Doctoris. A VMD degree is currently only conferred on veterinarians who have attended the University Of Pennsylvania School Of Veterinary Medicine in Philadelphia, PA.

Is there a difference between DVM and VMD? ›

Nope, not a typo. For 29 of the 30 veterinary schools in the United States, the designation is DVM, which stands for Doctor of Veterinary Medicine. But for graduates of the veterinary school at the University of Pennsylvania, the designation is VMD, or Veterinary Medical Doctor. The two are equivalent.

What does Intel VMD controller do? ›

Intel® VMD is an Intel® Xeon® Scalable processor feature that enables direct control and management of NVMe SSDs from the PCIe bus without additional hardware adaptors. This robust NVMe SSD functionality allows a seamless transition to NVMe storage while limiting the downtime of critical infrastructure.

What is the role of the accredited Internet Retailer scheme? ›

Accredited internet retailer scheme (AIRS)

AIRS is a voluntary scheme launched by the VMD to facilitate self-regulation by UK based internet retailers and compliance with the Veterinary Medicines Regulations.

Is a VMD a doctorate? ›

The Doctor of Veterinary Medicine (DVM) is a fully accredited rigorous four-year professional program preceded by three to four years of pre-professional studies.

What is the #1 vet school in the US? ›

University of California--Davis

Which country is best for veterinary Doctor? ›

Top 9 Highest-Paying Countries for Veterinarians
  1. USA. As noted above, the median annual salary of veterinarians living in the United States is $88,490.
  2. Netherlands. The average salary is $69,244 per year for veterinarians. ...
  3. Switzerland. ...
  4. Iceland. ...
  5. Qatar. ...
  6. Canada. ...
  7. Germany. ...
  8. Luxembourg. ...
13 Feb 2017

Which vet school is the hardest to get into? ›

The University of California Davis veterinary college is probably the hardest vet school to get into in the US. The program is ranked #1 in the country and has generally high admission stats and a competitive applicant pool.

Which is harder vet school or med school? ›

Though aspiring med students have to take the MCAT before applying to medical school, most people agree that vet school is harder than medical school. Vet school isn't harder because it requires more strenuous work.

What is the most prestigious vet school? ›

University of California at Davis

What is VMD storage? ›

Intel VMD is a storage controller with hardware logic inside Skylake CPU, which helps manage and aggregate NVMe SSDs. It behaves as an "integrated end point" to Skylake root complex, so OS/BIOS enumeration stops at the Intel VMD controller.

What is VMD raid? ›

Overview. Intel® VROC (VMD NVMe RAID) is a powerful, reliable, and affordable hybrid RAID solution that uses the built- in processor's Volume Management Devices (VMD) and Intel® RSTe drivers to create and manage RAID configurations. Intel® VROC is only available when the system is configured for UEFI boot mode.

Is Intel VMD needed? ›

Without Intel VMD, these events are handled, with varying degrees of success, by a combination of a system's BIOS and operating system. Intel VMD ensures smooth additions and removals of NVMe drives from the PCIe bus, which helps improve uptime and serviceability.

What are the four legal classifications of veterinary medicines? ›

prescription only medicine – Veterinarian (POM-V) prescription only medicine – Veterinarian, Pharmacist, Suitably Qualified Person (POM-VPS) non-food animal – Veterinarian, Pharmacist, Suitably Qualified Person (NFA-VPS) authorised veterinary medicine – General Sales List (AVM-GSL)

What does POM VPS stand for? ›

Prescription Only Medicine – Veterinarian, Pharmacist, SQP (POM-VPS)

Who regulates animal medication? ›

Animal Drugs– The Federal Food, Drug, and Cosmetic Act gives FDA the legal authority to approve and regulate drugs for animals. Before a drug company can market an animal drug, the company must get the drug approved by FDA.

Videos

1. Visualization and analysis with VMD — David Winogradoff
(TCBG UIUC)
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5. How to generate publication quality figures using PyMol
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