Dear all,
Sorry for not being able to describe my question properly in the title.
I just finished 100 ns simulation with GROMACS for my molecule, and I visualized the trajectory in VMD. The input files were .gro and .xtc (PBC removed), and I did not do anything else except for generating the movie.
I wonder why is my molecule flipping so fast in different directions, unlike other examples shown in YouTube tutorials? I googled 'how to fix the direction' but did not find the solution. Could anyone please help me with it?
Also, how could one find the appropriate frames for the molecule when writing .mdp file in the simulation? I feel like I should increase the number of frames for easier observation.
Dear Tini Chu
What do you mean by fast? What is the time scale of your video, that is, how much steps (and therefore simulations time) per frame? For example, if you have just 10 frames for 100ns then you are plotting one snapshot of your systems every 10ns, which could explain the dynamics you see.
You can modify the frame rate by changing the output values for the output options (https://manual.gromacs.org/documentation/current/user-guide/mdp-options.html#output-control) nstxout and/or nstxout-compressed in your mdp file, depending on what you are saving (full .trr binary or compressed .trj file respectively). The frame frequency is a trade-off among what you need to visualize/analyze and the amount of space available. Usually it is better to output the (reasonably) most you can, and in case discard data later. You can always reduce the number of frames by using GROMACS's native tools (such as gmx trjconv -skip) or other software, such as VMD.
Furthermore, VMD usually produces videos with rotation, you have to manually turn it off when rendering the whole thing. If you didn't, double check the output options when generating the video in VMD window.
Best,
Nicola
Dear Tini Chu
I agree with both the answers, but you again check with the command you provided for the boundary condition. Also, you can increase the frame size and, while exporting the movie, need to fix the issues.
I faced such a problem, but that got resolved after the system restarted.
Thank you all for the support! I tried the command -pbc nojump. It stopped flipping but somehow the molecule got extended at the end. I’m finding possible reasons...
I also modified the mdp file to increase the frame by 10 folds first. (finding the appropriate number of frames might be an interesting topic)
Shaban Ahmad Hello Sir, did you also try -pbc nojump when solving the problem?
Nicola Piasentin Excuse me Sir, what do you mean by the option to turn of the rotation in VMD? I checked the Renderer and the Movie Settings in the Movie Generator extension, but I didn’t find such an option. I used “Snapshot” for renderer and “Trajectory“ for movie settings to generate the movie attached to this page. cou you please give me some hints?
Dear Tini Chu
No your procedure seems correct to me. I remember some 'Rock&Roll' option for VMD which kinda of tilted the video, if I am not mistaken, but the 'Trajectory' option should work fine.
Thank you all for the support. Sorry for the late update. I just found how to deal with this problem. Just to record here in case someone is also interested in this info.
Still do it in VMD. Extension > Analysis > RMSD Traj tool
and then fix the backbone and click the 'align' button. Everything will be finer then!
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