Construction Of Windows Based On Energy
Project description
Construction Of Windows Based on Energy - COWBOE
This package consists of the "COWBOE" algorithm to construct windows on the reaction coordinate based on the test PMF values.
Installation
Run the following to install
''' pip install cowboe
'''
Module for optimization and selection of parameters for umbrella sampling
##################################################
COWBOE - Construction Of Windows Based On Energy
##################################################
Current settings for the module are as follow
"PMF unit" : r'PMF - Kcal / (mol $\cdot~\AA^2$)' "reaction coordinate unit" : r'$\AA$' "polynomial fit order" : 12 "param B" : 2.0 "Number of datapoints" : 100000 "conventional force constant" : 7 "conventional window width" : 0.5 "conventional no of windows" : 24 "conv. min of 1st window" : 2.5 "conv. min of last window" : 14.5 "fill colour" : 'r' "NM_alpha" : 1 "NM_gamma" : 2 "NM_beta" : 0.5 "NM_delta" : 0.5
To update any settings, use dict.update() e.g. cowboe_settings.update({"param B" : 2.0001})
usage
from cowboe import pmftopoints, cowboe, cowboefit, cowboeNM, NMprogress, cowboe_settings
cowboe_settings.update({"param B" : 2.0})
A = [2.0, 2.9, 3.5] V = [0.75, 0.8700, 0.8000] fit = [21.2642, 17.6376, 24.5880]
pmftopoints(testpmf='test_pmf.txt')
cowboe(A=2.84, V = 0.895 , sc =8)
cowboefit(test='1.txt',bench='bench.txt')
cowboeNM(A = A, V = V, fit = fit)
NMprogress(progressfile = 'progress.txt')
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
