VMD Visual Molecular Dynamics is a molecular visualization and analysis program designed for biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. This unit will serve as an introductory VMD tutorial. Among molecular graphics programs, VMD is unique in its ability to efficiently operate on multi-gigabyte molecular dynamics trajectories, its interoperability with a large number of molecular dynamics simulation packages, and its integration of structure and sequence information.
No limits on the number of atoms, molecules, or trajectory frames, except available memory. Before staring, the current version of VMD needs to be downloaded. This tutorial was written for VMD version 1. Follow the instruction online to install. This unit contains six sections.
Visualizing trajectories with Python, VMD, and .vtf files
For readers with no prior experience with VMD, we suggest they work through the sections in the order they are presented. Readers already familiar with the basics of VMD may selectively pursue sections of their interest.
Several files have been prepared to accompany this tutorial. You need to download these files HERE.
Using VMD - An Introductory Tutorial
In this section the basic functions of VMD will be introduced, starting with loading a molecule, displaying the molecule, and rendering publication-quality molecule images.
This section uses the protein ubiquitin as an example molecule. Ubiquitin is a small protein responsible for labeling proteins for degradation, and is found in all eukaryotes with nearly identical sequences and structures. When VMD loads a molecule, it accesses the information about the names and coordinates of the atoms. Then, one can explore various VMD visualization features to get a nice view of the loaded molecule.
The first step is to load the molecule. The pdb file, 1ubq. Start a VMD session. The Molecule File Browser window Figure 2 b will appear on the screen. Use the Browse… Figure 2 c button to find the file 1ubq. When file is selected, you will be back in the Molecule File Browser window.
In order to actually load the file, press Load Figure 2 d. Now, ubiquitin is shown in the OpenGL Display window. Close the Molecule File Browser window at any time.
Just type the four letter code of the protein in the File Name text entry of the Molecule File Browser window and press the Load button. VMD will download it automatically. In order to see the 3D structure of our protein, the mouse will be used in multiple modes to change the viewpoint. VMD allows users to rotate, scale and translate the viewpoint of the molecule. In the OpenGL Display, press the left mouse button down and move the mouse. Explore what happens.
This is the rotation mode of the mouse and allows for rotatation of the molecule around an axis parallel to the screen Figure 3 a. Rotational modes. A Rotation axes when holding down the left mouse key. B The rotation axes when holding down the right mouse key. Holding down the right mouse button and repeating the previous step will cause rotation around an axis perpendicular to the screen Figure 3 b.
Here, the user is able to switch the mouse mode from Rotation to Translation or Scale modes. It is now possible to move the molecule around when you hold the left mouse button down. Go back to the Mouse menu and choose the Scale mode this time.This requires a VMD installation not older than version 1. CMake will find the vmd executable in your path, and from it, or the environment variable VMDDIR at configuration or run time, locate the plug-ins.
Note that these plug-ins are in a binary format, and that format must match the architecture of the machine attempting to use them. In addition, the user can interact with the simulation by pulling on atoms, residues or fragments with a mouse or a force-feedback device. The group is specified via the mdp option IMD-group. To interact with the entire system, IMD-group can be set to System.
When using gromppa gro file to be used as VMD input is written out -imd switch of grompp. The port for the connection can be specified with the -imdport switch of mdrunis the default.
VMD permits increasing or decreasing the communication frequency interactively. By default, the simulation starts and runs even if no IMD client is connected. This behavior is changed by the -imdwait switch of mdrun.
After startup and whenever the client has disconnected, the integration stops until reconnection of the client. When the -imdterm switch is used, the simulation can be terminated by pressing the stop button in VMD. This is disabled by default. Finally, to allow interacting with the simulation i.
Therefore, a simulation can only be monitored but not influenced from the VMD client when none of -imdwait-imdterm or -imdpull are set. However, since the IMD protocol requires no authentication, it is not advisable to run simulations on a host directly reachable from an insecure environment.
Secure shell forwarding of TCP can be used to connect to running simulations not directly reachable from the interacting host. Note that the IMD command line switches of mdrun are hidden by default and show up in the help text only with gmx mdrun -h -hidden. In the IMD connection window, hostname and port have to be specified and followed by pressing Connect. Detach Sim allows disconnecting without terminating the simulation, while Stop Sim ends the simulation on the next neighbor searching step if allowed by -imdterm.
The timestep transfer rate allows adjusting the communication frequency between simulation and IMD client. Embedding proteins into the membranes. Quick search. Created using Sphinx 1.As a computational scientist who develops Brownian Dynamics BD simulations, I have had a difficult time finding software to visualize trajectories from my simulations. For storing the output of molecular dynamics MD simulations, this is logical, since the simulations often run for millions of time steps and it would be impractical to store and view all of them.
The user is often interested only in finding the lowest-energy configuration, so all the earlier steps can be discarded.
While this is also somewhat true for BD simulations, for debugging purposes it is helpful to visualize the trajectory of the particles. My first attempt at visualization was to use the free visualization package VMD. VMD is an industrial-strength tool designed to visualize the output of molecular dynamics simulations.
The user interface is not the best, and the license restricts usage of the free version to non-commercial use, but it seems to be very powerful and I have come nowhere near exploring its limits. VMD reads many different file formats, and allows the user to animate a trajectory and export it as a movie. This leads to the important question of choosing which file format to use to feed data into VMD.
Since I am writing my own simulation software, I want to choose a format that is standardized, well documented, easy to create, and supports multiple time steps. I found the. For my application, the animation capabilities of VMD are its best feature. VMD allows you to add arbitrary shapes to the view, but it has to be done with Python or Tcl scripting. The scripting interface utilizes a command-line console that is, by default, in Tcl mode. You can write your own modules and import them.
However, I did not find the Python interface to be particularly intuitive or well documented. I ultimately moved away from VMD because of its limited ability to add supplemental graphics. I wanted the capability to add a vector to each molecule to illustrate the net force on the molecule, and this proved to be too difficult with VMD. Another problem is that the. Your email address will not be published.
Notify me of new posts by email. This site uses Akismet to reduce spam. Learn how your comment data is processed. Skip to content As a computational scientist who develops Brownian Dynamics BD simulations, I have had a difficult time finding software to visualize trajectories from my simulations. Advantages For my application, the animation capabilities of VMD are its best feature.
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Please provide the ad click URL, if possible:. Help Create Join Login. Operations Management. IT Management. Project Management. Services Business VoIP. Resources Blog Articles Deals. Menu Help Create Join Login. Re: [lammps-users] How to view lammps trajectory by VMD. Oh no!
Some styles failed to load. Sign Up No, Thank you. Thanks for helping keep SourceForge clean. X You seem to have CSS turned off. Briefly describe the problem required :. Upload screenshot of ad required :. Hi Zhimin, You can also dump to the dcd format, which is the native format for the Charmm and NAMD molecular dynamics programs, or the xtc format, which is a compressed format native to Gromacs.
An additional advantage is that the trajectory sizes are smaller since it's a single precision binary format. However, the dcd and xtc formats only contains atomic positions, and you must dump all the atoms in your system since the atom tag information is implicit in the position index. To use the dcd format, dump positions dcd atom filename.
No limits.Note: These tutorials are meant to provide illustrative examples of how to use the AMBER software suite to carry out simulations that can be run on a simple workstation in a reasonable period of time. They do not necessarily provide the optimal choice of parameters or methods for the particular application area.
Copyright Ross Walker By Ross Walker. Updated for VMD 1. Note: Unfortunately VMD cannot yet load compressed gzipped trajectory files so when you download the nc. Lets start by loading some trajectory files covering the first 10ps of a molecular dynamics simulation of the TRPCage extended structure shown above.
These simulations were run using Sander v8. Here are the files you will need: TRPcage. If VMD is running, quit it. This way we should be starting from the same point. Into this structure we will load the two trajectory files, one after the other. So, load the first one, browse for heat1. Note: There are two types related to Amber trajectory nc files.
When sander writes an nc file from a simulation run with periodic boundaries, it writes an extra 3 floating point numbers to the end of each frame which are the box size. VMD is not smart enough to work out what type of trajectory file it is, so we need to tell it.
You can often tell if you have selected the wrong format because things will look very weird. Feel free to try it. If you do load a simulation that looks strange, try deleting the molecule and reloading it, selecting the other format:. Next click Browse again and find heat2. Load this in the same way you don't need to reload the prmtop file. Make sure TRPcage.
This will append the frames in heat2 to the frames we have already loaded. In this way, you can load a number of different trajectory sets into a single animation so that you can watch the full trajectory without interruption. You should now have frames of TRPcage loaded. This covers 10ps of heating from 0K to K.VMD Visual Molecular Dynamics is a molecular visualization and analysis program designed for biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc.
Among molecular graphics programs, VMD is unique in its ability to efficiently operate on multi-gigabyte molecular dynamics trajectories, its interoperability with a large number of molecular dynamics simulation packages, and its integration of structure and sequence information. The aim of this tutorial is to very quickly get you familiar enough with VMD to be able to view individual protein structures and the sorts of trajectories containing many structures that are produced by molecular dynamics and other simulation techniques.
This document is deliberately designed to cover only the most basic features of VMD. Excellent tutorials teaching the full range of the functionality provided by the program can be found at the VMD website, here. If you don't currently meet the last two criteria then follow the instructions in the next two sections. If VMD is not already available on your computer then you will, obviously, need to install it.
You just need to register with your email address and then download the appropriate package from here. Full installation instructions are available herebut the Windows and OS X installations are pretty self explanatory.
In this section we will load a single structure from a PDB and learn how to view it from different angles and to alter the way it is rendered on screen. Notice that once the molecule is loaded basic information including the name of the file and number of atoms appear in the Main window. A larger array of options for how the mouse interacts with the molecule shown in the OpenGL Display.How to make HD movies using VMD
We will concentrate on the first four options: rotate mode, translate mode, scale mode and center. The keyboard shortcut for each option is shown next to the choice in the menu for example pressing 't' when the OpenGL windows is selected will change into translate mode. By default VMD uses the rotate mode. Generally, to change the viewpoint you need select the OpenGL Display windows, hold the left mouse button and move the mouse the right mouse button can be used in rotate mode, see below.
Have a play with all of the modes below until you feel comfortable changing the view and switching between the various modes. You can easily tell which mode you are in because each one has a distinctive cursor Figure 6. Rotate mode : With the left mouse button held moving the mouse horizontally rotates the molecule around the vertical axis, up and down around a horizontal one.
When the right mouse button is held then the rotation is performed around an axis running into and out of i. Translate mode : When you hold down the left mouse button you can now move the molecule up, down, left or right in the viewing plane. Scale mode : Moving the mouse left or right whilst holding the left mouse button zooms in and out.
Center : The centre option is not a direct method for altering the view point. It is used to pick a point about which to perform a rotation. Once you have selected a center point change to Rotate mode to perform the rotation.Here we will learn to use VMD to examine a trajectory the same way we used it to examine a static structure in the Representations section.
You may be wondering, "If I'm using their files, why you shouldn't I be using their tutorial instead of this one? Click Browse, open 1UBQ. PDB, and click load. Next, load ubiquitin. Then click load. Now, you will load the trajectory into the current molecule.
Make sure the Load files for dropdown says "1: ubiquitin. Now browse for your trajectory file pulling. Now we will discuss the animation controls. The animation controls are all located at the bottom of the main window. Here is a brief outline of what they do.
Play around with the animation controls to get a feel for them. Once you are finished we will set up a representation that will make viewing the trajectory most informative. First hide 1UBQ. Now open the Representations window. Make sure "1: ubiquitin. Now delete the existing representation and create the following:. This will show where hydrogen bonds are. This is useful for seeing how secondary structure is pulled apart.
How to Use Visual Molecular Dynamics (VMD)
Feel free to play with the various settings. I used:. Molecules such as ubiquitin have structural elasticity that arises from hydrogen bonds found in their secondary structure. It is reasonable to assume that the extended beta sheet will be important in this molecule's unfolding. Here we will label each beta strand with alternating yellow and orange coloring in order to see the unfolding process easier. We will do this using a feature called the Sequence Viewer.
Go to Extensions in the main window, then to Analysis, and then click on Sequence Viewer.