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Installing MSMS for VMD

vmd sets LD_LIBRARY_PATH itself. If there is a problem with wrong versions of shared libraries, copy them into the vmd lib directory, and vmd will find them.

Running vmd

A great resource is the user manual [1].

One can run scripts in VMD command line (example scripts).

To run a script (in windows) type source in the command line followed by the fill name.

Useful atom selection commands:

"within <distance> of <selection>" 
"same <property> as <selection>"
same resid as within 5 of resname LIG

Example Scripts for VMD

here is a script to calculate rmsd's: vmd.rmsd.csh.