compute_density 1.0 ------------------- REQUIREMENTS: VMD Version 1.9.4 or greater DESCRIPTION: Computes the overall mass density (g/cm3) per frame from a NAMD trajectory. Requires a PSF and DCD loaded in VMD with periodic cell info. Handles both orthorhombic and triclinic unit cells using the general triclinic volume formula. Outputs per-frame density, volume, and cell dimensions to a file, along with an average density summary. PROCEDURES: compute_density - takes two arguments: the molecule id and the output filename EXAMPLE USAGE: # Load your system mol new system.psf mol addfile trajectory.dcd waitfor all # Compute density for the top molecule source compute_density.tcl compute_density top "density.dat" DOWNLOAD THE FILE: compute_density.tcl AUTHOR: Diego Enry Barreto Gomes (dgomes@auburn.edu)