simtk.org

Hi All,
I am new to this, i have started working using Zypher tool. I have simulated a protein successfully and got an output now i need to visualize the output file.
can any one suggest the best visualization tools.

Zephyr is just running Gromacs, so I assume that you are getting either .trr or .xtc files for the outputs of your trajectories. If you take a look at the Zephyr User's Guide, there is an extensive section on pairing it with VMD, which is an excellent tool for visualizing molecular dynamics simulations and molecular structures in general.

I would recommend reading the manual since it explains the various output files and how to connect up to VMD (or you can take the output files and load them directly into VMD).