Vmd load dcd file

So, please help me how to resolve this issue. Yes, indeed. Try what Lars has suggested. Also, make sure you have proper suffix for your DCD file. Thank you for your suggestions. I have the following input when I loaded the files on vmd. One more thing. It's just popping up empty without generating any plots. Do I need to install Xmgrace for this to visualize the plot?

Kindly advice. For example, if your DCD contains C-alpha atoms only, try. Read VMD manual please and you may find answers. I am also facing a similar problem of loading. I got a following error. Any suggestions why it is not loading the no. Note: file size is 3. Can you open the. Then, try again with bio3d to read the new. Let me know what you get. Yes I can open the.

I followed your instructions. Very often, the file auto-detect in VMD gets the file type wrong, so you should always check to make sure this is set to the correct filetype. When you are done, you should see a roughly cubical box of butanes. Go ahead and represent them however you want. Or, the simulation may have saved data every 10 timesteps, and you want to cut it down to every or timesteps.

In these cases, you may want to skip some regular number of frames. This is easy to do while loading. In the example below, I am going to load every 10th frame of the whole trajectory. Viewing the trajectory Now you can view the trajectory, movie-like, by clicking on the play button see below.

The difference from the loading step is that these frames are still there, they are simply not viewed. So any analysis, statistics, etc. Smoothing versus eliminating frames The real answer to making the movie look smoother is found under the Graphical Representations menu.

This allows interpolation of the moves, averaged over the number you set here. Once this is set, you should find you are able to follow individual butane molecules around the box. You may notice some molecules disappearing from one side, and reappearing on the other. This is due to periodic boundary conditions.

Simply put, periodic boundary conditions PBC tries to simulate many more molecules than you are actually using by replicating the simulation box with periodic images in all directions.

In two dimensions, this is like putting your simulation box at the center of a checkerboard, and making copies of that box to fill the other checkerboard squares. Thus, when a molecule leaves the box in one direction, it re-enters the box on the opposite side.

VMD can account for this by displaying periodic images, something we will work with later on. Simple dynamic analysis via labels The simplest way to begin to use VMD to analyze trajectories is through labels. We saw labels earlier, but now they become more useful. This trajectory has 10, frames, which is probably too much at first glance.

This will have something to do with the helical nature of this peptide, as a nicely-formed helix will be longer than a random coil. For picking out individual atoms, CPK is probably the best representation. Now if you run the trajectory, this distance will adjust as the atoms move about. This end-to-end length information is nice to see on screen, but what if we would like to plot the data separately? The minimum and maximum values are labeled along with the trajectory frame number.

You have two other options here. Any other sort of information that can be labeled may be plotted in this way. Time-evolution of structural details can be followed by using dynamic RMSD. Here we will compare two similar peptides, ek12 and ck The only difference is that ck12 has an N-terminal cysteine in place of an alanine in ek Notice that there are several new choices here, related to the trajectory.

These should be straightforward to figure out with our experience. The choices below are related to trajectories. The reference frame can be set, along with a skip stride interval. The time can also be set for plotting ; these times are in femtoseconds.