VMD plugin directory not found.Please compile the VMD plugins and do 'make distrib' to copy them...
You need to have the Swap plugin installed to see these options. It does not work with ALIGN. verbose will print the out the status of the swapped atoms during the RMSD calculations to the console. List will print out the current definitions to the console. Weights Calculated a weighted ...
You can use the absolute or relative path, including '.' for the local directory. Or, if you have installed qwrap as a VMD plugin: package require qwrap You can now use theqwrapandqunwrapcommands. Usage To use in VMD: qwrap [first n] [last n] [compound none|res|beta|fragment [...
NMWiz will try to find the path to Python executable ('python' or 'python.exe') and ProDy script ('prody'). For this to work, both of these files must be in you PATH environment variable. If they are not found, you will be prompted to specify the path. ANM/GNM Settings --- Spe...
This directory contains utility scripts for using VMD to visualize and analyze LAMMPS trajectories (hopefully in the future this will turn into a plugin or proper library). Below are short descriptions and examples on how to use them. Additional information on VMD as well as additional scripts ca...
To use the Clustering plugin you need to: Load a trajectoryof conformations used for clustering into VMD. Define theatom selectionand molecule to use as representation in vmd. Generatethe clusters with VMD's internal measure cluster command. More information aboutmeasure clustercan be found in VMD...