This script adds molecules in random positions above or below a membrane using Poisson disk sampling (https://en.wikipedia.org/wiki/Supersampling#Poisson_disc) to make sure points are not close to each other. All files concerining this cript are in the 'insertion' folder
Requires mdanalysis and cython among other dependencies which can be intalled as follows:
pip install mdanalysis
pip install cython
Following this the cython portion of the program can be installed as follows
python setup.py build_ext --inplace
The example script can be run as follows:
python above_membrane.py molecule.gro membrane.gro -d -2.5 -ms "resname POPE POPG CDL2" -n 6 -o test.gro
A description of the options availble can be found using
python above_membrane.py -h
This script parses the output of umbrella sampling files in gromacs and runs Weighted Histogram Analysis Method using either the method included within gromacs or the Grossfiled implementation (see http://membrane.urmc.rochester.edu/?page_id=126). Note that this script is only a python wrapper for both implementions. All files concerining this script are in the 'umbrella' folder.
Requires gromacs versions > 5 and for the grossfiled wham implementation obtained from http://membrane.urmc.rochester.edu/?page_id=126 to be complied as follows
cd wham
make clean
make
The example script can be run as follows:
python parse_pull_files.py -pxn umb_prod -p test_data/ -op test -s 1:41:0:2000 -skip 2 -n_jobs 6 --zprof0 4.8 --keep
A description of the options availble can be found using
python parse_pull_files.py -h