About

Python scripts used for dissipation corrected targeted molecular dynamics analysis for usage with "*pullf.xvg" files from Gromacs v2016 or higher (Application of usage with Gromacs v5.X and lower only needs adjustment in the "skiprows" argument in the data read in step).

• NEQGamma.py: Integrates a constraint force file via trapezoid rule, calculates the NEQ memory friction kernel and friction factors, and performs a friction correction. Use "-h" for more information on usage. ATTENTION: Use with python3 or higher!

• NEQJarzy.py: Integrates a constraint force file via trapezoid rule, and performs a friction correction based on Jarzynskis fast growth estimator (see Hendrix, D. A. and Jarzynski, C. J. Chem. Phys. 114, 5974 (2001)). Use "-h" for more information on usage. ATTENTION: Use with python3 or higher!

Licensing

If you use the scripts for published works, please cite as:

Wolf, S., & Stock, G. (2018). Targeted Molecular Dynamics Calculations of Free Energy Profiles Using a Nonequilibrium Friction Correction. J. Chem. Theory Comput., 14, 6175–6182.