Repository with various scripts used for molecular dynamics. The scripts are usually designed with a single purpose and need to be modified for any other use.
Most of the scripts require pyvmd library and they can be well combined with the md-project-template.
A Python script to download a sequences of human TRP channel tails from UniProt database.
A Python VMD script to generate a model of a TRP channel from a PDB file.
A Python VMD script to generate constraints for a simulation of a TRP channel.
A Python VMD script to generate constraints for a MDFF simulation.
A Python VMD script to collect distances of pairs of atoms over a trajectory.
A Python VMD script to parse FEP simulation output.