I've a gromacs trajectory of 500 ns whose size after removing the solvent is about 2 GB. I want to generate a movie highlighting certain residues, I tried Chimera, it crashed and couldn't even load the trajectory. I tried VMD, it did load the trajectory and I highlighted what I want, however it crashes due to memory error after rendering few frames (I just selected the simple snapshots method, not ray-tracing, and I tried to increase the step size many times).
Any suggestions to generate a molecular dynamics simulation movie for such a large-sized trajectory?
1. Reduce the trajectory size with the built-in tool "gmx trjconv", commands like" -b -e -dt -skip" might help.
2. Try it on a computer with a larger RAM.
Marwa Abd El Kader Zaater i think you can generate small videos (100 frames for each one, for example) then combine it using any video editor
VMD (vmd script) >>> PDBs >>> PyMOL (python script) >>> PNGs >>> GIMP >>> animated GIF (30 frames should be enough to illustrate an observation)
You need to provide more information
Linux or windows,
VMD version
size of your RAM.
how many atoms what representation do you use. what rendering you have done
See this, it might be helpful;
https://www.youtube.com/watch?v=qz6j4w-JGw0
For this case, you can use VMD or Pymol on Linux or windows. Simply, you can generate target frames using the gmx relevant commands, then open the frame via pymol or VMD and watch the modification confirmation during target simulation time frames. You can save the movie and then use it for your publication. Please note that if you use PyMOL for generating movie clips of MD simulations, you had to install FFmpeg plugin in ubuntu. To do this:
$ sudo apt-get udpate
$ sudo apt install ffmpeg
$ ffmpeg -version
$ ffmpeg version 3.4.4-0ubuntu0.18.04.1 Copyright (c) 2000-2018 the FFmpeg developers built with gcc 7 (Ubuntu 7.3.0-16ubuntu3)
Then, open target MD frames in your pymol menu. Select file> export movie as> select target format and save the movie.
In VMD:
First, try to extract your target frame from the gromacs output md.xtc and md.tpr using the following command:
$ gmx trjconv -f md.xtc -s md.tpr -b -e -o snapshots.pdb
You should select your target MD time frame, e.g.,:
$ gmx trjconv -f md_0_1.xtc -s md_0_1.tpr -b 10000 -e 25000 -o snapshots.pdb
The above-mentioned command will provide you with the target snapshots of favorite time frames. Then open VMD and:
1- Load the molecule
2- Go to the Analysis tab and select the movie maker module.
3- Select the format and specify your own options.
4- Click on make movie and wait until it makes the movie.
No, you can see the conformational changes of your structure. For other options in VMD, you can see its developer tutorial on how you should use MD trajectories for this purpose.
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