dcTMD¶
Calculate free energy and friction for given constraint force files.
| dcTMD |¶
Analysis tools for dissipation-corrected targeted molecular dynamics, which is an enhanced sampling method to enforce rare events in biomolecular systems. When publishing results gained with this python package, please cite the following publications: (1) Tänzel, Victor and Jäger, Miriam and Wolf, Steffen in preparation. (2) Wolf, Steffen, and Gerhard Stock. 'Targeted molecular dynamics calculations of free energy profiles using a nonequilibrium friction correction.' Journal of chemical theory and computation 14.12 (2018): 6175- 6182.
Usage:
Options:
-m, --mode [work|force] Use either work or force autocovariance function to
calculate dcTMD quantities. [default: work;
required]
-f, --file TEXT Input: File containing list of all constraint force
file names or glob pattern e.g."*.xvg" to generate
a list of all constraint force files using
glob.glob() [required]
-o, --outname PATH Output: Path/prefix of output names.
-T, --temperature FLOAT Simulation temperature in K. [required]
-vel, --velocity FLOAT Pulling velocity in nm/ps. [required]
--res INTEGER Striding to reduce size of returned free energy and
friction. [default: 1]
-s, --sigma FLOAT Standard deviation of gaussian filter in nm.
-v, --verbose Enable verbose mode.
-p, --plot Plots free energy and smoothed friction.
-sd, --save_dataset Save the Work/ForceSet instance to file.
--help Show this message and exit.