Template_colvar Directory

This directory contains template files for calculating alpha scores of peptides using VMD's Colvars module. For detailed documentation on the alpha score collective variable in Colvars, refer to the Colvars Reference Manual.

Files

• template_colvar.tcl: Tcl script for running the analysis
• template_colvar.inp: Colvars configuration file

Usage

1. Edit the input variables in template_colvar.tcl:

   set psf_file "path/to/your/structure.psf"  # Your PSF file
   set traj_dir "path/to/your/trajectories/"  # Directory with DCD files
   set output_file "colvar_output.dat"        # Output file name
   set colvar_config "colvar.inp"             # Colvars config file

2. Edit template_colvar.inp to match your system:

   • Update psfSegID to match your peptide's segment name
   • Adjust residueRange to include the residues you want to analyze
   • Modify boundaries if needed (default: 0.0 to 1.0)

3. Run the analysis:

   vmd -e template_colvar.tcl

Output

The script generates a data file with three columns:

• Frame number
• DCD filename
• Alpha score value

Notes

• The alpha score is calculated using VMD's Colvars module
• Values are clamped between 0.0 and 1.0 for histogram purposes
• Make sure your PSF file has the correct segment names and residue numbering