# JCTC Paper Published

Our paper titled “Solvation Structure and Thermodynamic Mapping (SSTMap): An Open-Source, Flexible Package for the Analysis of Water in Molecular Dynamics Trajectories” has been published in the Journal of Chemical Theory and Computation: DOI: 10.1021/acs.jctc.7b00592.

# Installing SSTMap

The main requirement for installation of SSTMap is the anaconda python distribution. If you are not familiar with Anaconda, please have a look at continuum.io/why-anaconda. SSTMap is implemented in python 2.7, so if you do not have the anaconda installation, downlaod the anaconda for python 2.7, as shown below. Alternatively, if you have a an anaconda installation for python 3.6, you can create a python 2.7 enviornment to run sstmap.

# Running SSTMap Calculations

SSTMap implements two approaches for mapping water structure and thermodynamics on to solute surfaces, such as protein binding sites, the hydration site analysis (HSA) and Grid Inhomogeneous Solvation Theory (GIST). The command lines to run each of these analyses are simply run_hsa and run_gist which are the main command-line tools in SSTMap. Here we provide examples of the command line arguments required to run these analyses with different popular MD packages.

Both run_hsa and run_gist output several files, which are named after the prefix specfied under -o flag. In this post, we will describe these outputs.