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https://github.com/vtlim/permeability
Adaptive biasing force (ABF) & umbrella sampling (US) simulations to calculate membrane permeability
https://github.com/vtlim/permeability
Last synced: 3 months ago
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Adaptive biasing force (ABF) & umbrella sampling (US) simulations to calculate membrane permeability
- Host: GitHub
- URL: https://github.com/vtlim/permeability
- Owner: vtlim
- License: mit
- Created: 2016-10-15T01:58:41.000Z (about 8 years ago)
- Default Branch: master
- Last Pushed: 2020-05-01T23:01:09.000Z (over 4 years ago)
- Last Synced: 2024-10-04T13:49:36.770Z (3 months ago)
- Language: Python
- Homepage: https://link.springer.com/article/10.1007/s00232-020-00149-8
- Size: 4.47 MB
- Stars: 5
- Watchers: 1
- Forks: 0
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# Calculation of membrane permabilities using molecular dynamics simulations
This document last updated: Feb 28 2019
This repository contains scripts for preparing and analyzing molecular dynamics simulations to calculate
membrane permeabilities via three approaches: (1) umbrella sampling, (2) adaptive biasing force, and
(3) a variant of adaptive biasing force called meta-eABF. Simulations are run using the NAMD software package.
Selected references:
1. (ABF, water) [Calculation of Lipid-Bilayer Permeabilities Using an Average Force](http://pubs.acs.org/doi/full/10.1021/ct400925s)
2. (eABF) [Smoothed Biasing Forces Yield Unbiased Free Energies with the Extended-System Adaptive Biasing Force Method](https://pubs.acs.org/doi/full/10.1021/acs.jpcb.6b10055)
3. (meta-eABF) [Zooming across the Free-Energy Landscape: Shaving Barriers, and Flooding Valleys](https://pubs.acs.org/doi/full/10.1021/acs.jpclett.8b01994)
4. (ABF vs. US) [Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds](http://pubs.acs.org/doi/full/10.1021/acs.jcim.6b00022)
5. [NAMD user guide for version 2.13](https://www.ks.uiuc.edu/Research/namd/2.13/ug.pdf)
-------------------------------------------------------------------------------------------------------
## Notes
* There is a Python module here called [`abf_pmf_processor.py`](analysis/permeability/abf_pmf_processor.py) which processes NAMD ABF PMFs. Functions include:
* Averaging overlapping gradients from separate windows
* Combining PMFs from separate leaflets
* Setting average bulk water region of PMF to zero
* Symmetrizing PMF (for symmetrization by anti-symmetrization of weighted gradients see [`symmetrize_profile.py`](analysis/permeability/symmetrize_profile.py))
* Computing error by deviation from unsymmetrized PMF
* Calculating pKa shift profile given two PMFs
* See examples located [here](analysis/permeability/examples/)
* The scripts for ABF are more up-to-date than the umbrella sampling ones, though all should be fully functional.
* There is a C++ script here called [`diffusivity.cpp`](US/diffusivity/1_fromSI/diffusivity.cpp) which calculates autocorrelation functions and diffusivity from NAMD traj files.
* I did NOT write this script; it is from the SI of ref. 4.
* The code here was extracted from the SI PDF, reformatted with proper spacing (fixing artifacts of copy/paste), and documentation was added.
## Directory tree
```
.
├── ABF
│ ├── 01_prep
│ │ └── plain_abf_files
│ ├── job_scripts
│ └── winmerge
├── analysis
│ ├── 01_area-box-lipid
│ ├── 02_density-profile
│ │ └── example
│ ├── 03_permeant-position
│ └── permeability
│ ├── archive
│ └── examples
│ ├── abf_pmf_processor
│ ├── calc_perme
│ └── matchX
├── US
│ ├── 01_setup
│ ├── 02_analysis
│ │ ├── 01_area
│ │ ├── 02_overlap
│ │ ├── 03_wham
│ │ └── 04_mbar
│ └── diffusivity
│ ├── 1_fromSI
│ └── 2_fblockavg
└── waterbox
27 directories
```