Making a movie to show the simulation results has became a more and more popular task in computational structural biology. However, the raw movies generated by many tools, including VMD, ffmpeg or mencode, do not support playing  .mp4 files in a Web browser. This is mainly because these tools do not support libx264 code by default.

The solution for this issue is also quite straightforwad: either use the static precompiled ffmpeg or recompile ffmpeg with two addtional options "--enable-libx264 --enable-gpl".

Once it is done, one can generate or convert a .mp4 file, which supports being played in a HTML5 Web browser, using command line:

ffmpeg -i out.ogv -c:v libx264 -c:a aac -strict experimental -pix_fmt yuv420p -movflags +faststart x.mp4