The code is at a reasonably stable state with many features added since the previous release (version 1.2). From this point forward I will implement the Thermo target (with pandas as a dependency) and add integration with MDTraj. Major: Engine class is a unified interface to MD simulation codes. Added Gromacs, OpenMM, and TINKER engines. Thermo target; simple support for general thermodynamic properties. (Erik) Lipid target; lipid bilayer properties. (Keri ForceBalance --continue option continues an aborted run and loads as much data as possible from the latest iteration. Parameter filtering allows targets to skip over parameters that are known to be irrelevant, for efficiency of finite difference derivatives. (Optimizer / Liquid / Lipid) Increase simulation length as we get closer to convergence. (Gromacs) Now supports binding energies, interaction energies, multipole moments and vibrational frequencies. (OpenMM) Now supports binding energies, interaction energies, and multipole moments. (nifty.py) exec_() reads from stdout and stderr asynchronously, allowing us to split the streams and tail -f the output at the same time. Minor: (Gromacs) Improved behavior of .mdp file editor (OpenMM) Force fields with virtual sites are now working. (OpenMM) AMOEBA-style force fields now work with virtual sites. (TINKER) Improved behavior of .key file editor (molecule.py) Read Q-Chem error messages (molecule.py) More decimals in GROMACS output coordinates (molecule.py) Fix to Kabsch alignment (molecule.py) Attempt simple repairs to object instead of crashing (molecule.py) TINKER 6.3 compatibility; reads/writes .arc files with/without periodic boxes (molecule.py) Delete symbolic link when attempting to write to one (molecule.py) Simple function for making water molecules rigid (molecule.py) Rebuild bonds when slicing by atom index (molecule.py) Improved topology building; uses grid search and rectangular MIC for finding contacts. (molecule.py) Methods for finding angles and dihedrals (molecule.py) Pathwise RMSD (i.e. each frame's RMSD from previous) (molecule.py) Try to figure out if .xyz is TINKER format or regular .xyz format (molecule.py) Expand tabs to spaces when reading files (molecule.py) Q-Chem output reader is more robust, reads IRC and FSM output (nifty.py) extract_int extracts representative integer value from floating point array (nifty.py) monotonic enforces monotonicity in a floating point array (nifty.py) multiD_statisticalInefficiency multidimensional wrapper to statisticalInefficiency (Keri) (nifty.py) Improved WQ interface and CCTools version 4.1 compatibility (nifty.py) click() provides simple timing (nifty.py) bak() provides simple file backup (nifty.py) onefile() searches for one file with a provided extension (nifty.py) wopen() deletes symbolic link when attempting to write to one (nifty.py) warn_press_key() only pauses when running interactively