Memory Down

AmberTools 16 together with Ipython notebook Amber (starting from 16) supports Ipython notebook (also known as jupyther notebook), which is useful for trajectories visulization and analysis and is very powerful tool to record your commands.  Besides the amber mdcrd trajectories, you may also use it to analyze your gromacs trajectories.  The strength of IPython notebook is that it is flexible and extendable and very user-friendly.  In case you'd like to try IPython notebook together with MD trajectory analysis, you could first read few pages about Jupyter notebook and AMBER pytraj. http://jupyter.org/ http://ambermd.org/tutorials/analysis/tutorial_notebooks/nglview_notebook/ http://ambermd.org/tutorials/analysis/ If you'd like to use it, these are useful step-by-step instructions for Pytraj with Ipython here : You need to install conda or anaconda first. See this link   https://docs.continuum.io/anaconda/install 1. login to your remote server or