ptc-cmc / cybercamp Goto Github PK

https://media.giphy.com/media/3o6gb3kkXfLvdKEZs4/giphy.gif

Current versions of VMD (1.9.4a) which are necessary as previous versions are 32 bit programs, cannot open gsd trajectory files. As such, VMD visualization in this notebook must be done using a different method. One recommendation would be to use a gsd plugin for VMD, https://github.com/mphowardlab/gsd-vmd, or to output a dcd trajectory (hoomd.dump.dcd()) and load in a topology as well for easy visualization.

The bevan lab vt link is no longer relevant - it has moved to http://www.mdtutorials.com/gmx/

The main README.md page has left over instructions on how to set up a Conda environment. However, this is also part of the setting_up_you_computer directory that we point to to include all of the steps for setting things up. We will want to consolidate this into one place.