You can also look harder into GROMACS tools, as they are quite complete. 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. o vmdmovie: Fixed a bug in the movie maker plugin that prevented movies from. Trj files are NOT the output of gmx dump. VMD can be used to animate and analyze the trajectory of molecular. In the Renderer we will chose 'Internal Tachyon', Movie settings: 'Trajectory', Format ‘MPEG-2, NTSC DVD’ and we click on the Make Movie. In the Name of the movie, write the name of the output file.
Vmd movie maker generator#
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. Extensions -> Visualization -> VMD Movie Generator We will select a path in our computer to save the movie using the ‘Set working directory’.
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