10.3.1 Download VMD and Manual
To download VMD and the documentation, please see the VMD website. Please note that VMD no longer supports OpenGL and therefore does not work on MacOSX from Catalina and newer (10.15 and on).
10.3.2 Using VMD with AMBER
tutorial acts as a brief introduction to using
VMD for visualising AMBER
inpcrd, restrt and trajectory files. While only scratching the surface of
what VMD can do it covers setting up a .vmdrc file to set the default layout
of VMD, loading static structures and performing RMSD fits between similar
structures. It then goes on to cover loading and visualising AMBER
trajectories, both from gas phase/implicit solvent simulations and from
periodic boundary simulations and shows how to save individual frames from a
trajectory as well as create an MPEG video of the trajectory.