Re: [gmx-users] unable to display MARTINI system with VMD

The problem is a mismatch in the contents of the .gro/.xtc and .psf produced by top2psf.pl. Since the script only handles one moleculetype, you can only display and/or read coordinates of that same moleculetype. So, to display properly: 1. Strip only the protein's coordinates from the .xtc

Re: [gmx-users] unable to display MARTINI system with VMD

John wrote: Hello, I have run a few protein systems through simulations of varying lengths and would like to find a way to visualize the trajectories. I have tried to use the top2psf.pl script to produce a usable .psf file. I can get it to produce the .psf file, but am u