7) Select and measure the angle between selected atoms. Information about the selected atoms will appear also at the vmd console window. The green label for selected atoms and additionally the white label with the distance (in Å) will appear (Fig. To switch-on the selection mode press 2 on the keyboard and then click on any two atoms. 6) Select and measure the distance between two atoms. This will state the molecule id, trajectory frame, atom name, atom type, atom index, 3Ĥ residue name, residue id, chain name, segment name and x, y, z coordinates of the selected atom. Simultaneously additional information at the vmd console will appear. The green label containing residue name, number and atom type will appear (Fig. To switch-on the selection mode press 1 on the keyboard and then click on any atom. If you come back to the rotation mode you will see that now the protein rotates around the chosen atom. To switch-on the center mode press c on the keyboard and then click left on the chosen atom. Scaling is also possible in the rotation or translation mode by rolling the middle mouse button. To switch-on the translation mode press s on the keyboard and then press the mouse left key and translate. To switch-on the translation mode press t on the keyboard and then press the mouse left key and translate. Usually the rotation mode is the default 2) Translate the protein. If it does not work press r on the keyboard to switch-on the rotation mode. In the VMD OpenGL display window the user can: 1) Rotate the protein. VMD OpenGL The VMD OpenGL (Fig.3) is the main graphic window in which the molecule is displayed. If the trajectory is loaded, this window allows the user to play, stop and pause the trajectory, to select a particular frame number to be displayed, to choose if the trajectory should be played once or in a loop or to change the speed (how fast the trajectory is played). To change T, A, D and F it is enough to double-click on them. Each molecule has its ID, T (Top), A (Active), D (Displayed) and F (Fixed) options, the information about number of atoms in the structure and the number of Frames loaded is given. 2) is a VMD control window, which contains all sub-menus and also shows all loaded molecules. You can also look harder into GROMACS tools, as they are quite complete.3 1. In this case I would recommend to instead look into some molecular dynamics python libraries, like MDAnalysis, PyTraj or MDTraj, which will also allow you to make minute modifications to the trajectory file while still reading it in its original format. Why would you absolutely need gmx dump output to be read by VMD? The only reason I can see is a handmade script doing modifications to your trajectory. trj was done by gmx trjconv, but I don't think this is possible anymore (see gmx trjconv supported trajectory formats in GROMACS 5 vs GROMACS 2021). In recent versions of GROMACS trj files are no longer supported, probably as they were not in a binary format, hence took too much disk space (see Trajectory files formats in GROMACS 2021 documentation). This is also why it tells you the header is wrong. trj files were used in "old" versions of GROMACS to store trajectories (see trj file format documentation of GROMACS 5), and this is what VMD is awaiting, not the output of gmx dump. Trj files are NOT the output of gmx dump. I don't think that the output of gmx dump can be read by VMD: the goal of this command is to provide a human-readable output, not to convert one trajectory format into another.
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