how to visualize the system

[UnixJunkie]

It would be nice to visually inspect the prepared system to answer some basic questions.

• Is the protein complete?
• Is it centered in the box and surrounded by water molecules?
• Is the box shape the one I chose?

Which software to use, which files to open? Maybe there is a chimera one-liner, but I don't know it. The tutorial doesn't mention anything about that.

I suspect that visualizing the network of hydrogen bonds before and after minimization of the system might be an interesting visual check.

[jalemkul]

Tutorials exist for all major visualization software, so I do not feel it necessary or even in the scope of these GROMACS tutorials to devote space to addressing those topics. I think it would become far too overwhelming for new users to try to develop all of these skills at once.