Tools for VMD

  1. Install VMD & Run at Console

  2. Build structures

  3. Make potential maps and field lines

  4. Make images and movies

  5. VMD Scripts

  6. Dihedrals and Ramachandranplot

Tools for NAMD

  1. Install NAMD at HPE SGI 8600

  2. Install NAMD at Cray-XC40

  3. Run NAMD on GPU

  4. NAMD Configuration File

Tools for R

  1. R Scripts

  2. Deploy R package on Github


  1. Download youtube video using chrome extension and choosing 8k UHD format
  2. Convert to gif: ffmpeg -i input.webm -pix_fmt rgb24 output.gif
  3. ffmpeg -i -pix_fmt rgb8 -r 10 output.gif && gifsicle -O3 output.gif -o output.gif