desolvate

pestifer desolvate generates DCD files that are stripped of solvent (usually water).

pestifer desolvate requires the name of a PSF file and any number of congruent DCD files (listed in chronological order). It assumes you want to strip out anything that is not protein or lipid, unless you specify a different VMD atomselect string to define the part of ths system you want to keep. It will generate a new PSF file and a single DCD that is the stripped version of concatenation of the input DCD files.

pestifer desolvate is really just a convenient wrapper for the catdcd command that comes with VMD.

For help with pestifer desolvate:

$ pestifer desolvate --help

Example

Say you have a PSF file my_system.psf and DCD’s generated from sequential NAMD runs called run01.dcd, run02.dcd, etc. A simple invocation of pestifer desolvate might be:

$ pestifer desolvate --psf my_system.psf --dcd-infiles run??.dcd

This will generate dry.psf and dry.dcd, which will hold all frames from the input DCD files stripped of everything but protein, lipid and nucleic acids, and any ligands.