Tcl scripts¶
These scripts are used by Pestifer for certain system preparation tasks. They are not intended to be run directly by users, but rather are used by Pestifer’s Tcl API.
domainswap.tcl¶
A VMD/TcL script to generate the ColVars configuration file necessary to perform a domain-swapping TMD simulation using NAMD colvars
bilayer_embed.tcl¶
VMD/psfgen script for creating a new psf/pdb pair for a complete, membrane-embedded protein pdb from an intact membrane system and the original protein psf/pdb
bilayer_patch.tcl¶
VMD/psfgen script for creating a new psf/pdb pair for a bilayer patch from a packmol pdb output
bilayer_quilt.tcl¶
VMD/psfgen script for creating a new psf/pdb pair for a bilayer created using the upper leaflet of one input bilayer and the lower leaflet of another, and replicated in x and y to make a “quilt”