{"id":15347384,"url":"https://github.com/vtlim/permeability","last_synced_at":"2025-04-15T04:13:06.347Z","repository":{"id":182914671,"uuid":"70959890","full_name":"vtlim/permeability","owner":"vtlim","description":"Adaptive biasing force (ABF) \u0026 umbrella sampling (US) simulations to calculate membrane permeability","archived":false,"fork":false,"pushed_at":"2020-05-01T23:01:09.000Z","size":4685,"stargazers_count":6,"open_issues_count":1,"forks_count":1,"subscribers_count":0,"default_branch":"master","last_synced_at":"2025-04-15T04:12:59.249Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://link.springer.com/article/10.1007/s00232-020-00149-8","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/vtlim.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2016-10-15T01:58:41.000Z","updated_at":"2025-02-25T07:07:03.000Z","dependencies_parsed_at":"2023-07-22T04:10:01.907Z","dependency_job_id":null,"html_url":"https://github.com/vtlim/permeability","commit_stats":null,"previous_names":["vtlim/permeability"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vtlim%2Fpermeability","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vtlim%2Fpermeability/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vtlim%2Fpermeability/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vtlim%2Fpermeability/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/vtlim","download_url":"https://codeload.github.com/vtlim/permeability/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":249003956,"owners_count":21196793,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-10-01T11:33:06.659Z","updated_at":"2025-04-15T04:13:06.331Z","avatar_url":"https://github.com/vtlim.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"\n# Calculation of membrane permabilities using molecular dynamics simulations\nThis document last updated: Feb 28 2019\n\nThis repository contains scripts for preparing and analyzing molecular dynamics simulations to calculate \nmembrane permeabilities via three approaches: (1) umbrella sampling, (2) adaptive biasing force, and \n(3) a variant of adaptive biasing force called meta-eABF. Simulations are run using the NAMD software package.  \n\nSelected references:\n1. (ABF, water) [Calculation of Lipid-Bilayer Permeabilities Using an Average Force](http://pubs.acs.org/doi/full/10.1021/ct400925s)\n2. (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)\n3. (meta-eABF) [Zooming across the Free-Energy Landscape: Shaving Barriers, and Flooding Valleys](https://pubs.acs.org/doi/full/10.1021/acs.jpclett.8b01994)\n4. (ABF vs. US) [Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds](http://pubs.acs.org/doi/full/10.1021/acs.jcim.6b00022)\n5. [NAMD user guide for version 2.13](https://www.ks.uiuc.edu/Research/namd/2.13/ug.pdf)\n\n-------------------------------------------------------------------------------------------------------\n\n## Notes\n\n* There is a Python module here called [`abf_pmf_processor.py`](analysis/permeability/abf_pmf_processor.py) which processes NAMD ABF PMFs. Functions include:\n    * Averaging overlapping gradients from separate windows\n    * Combining PMFs from separate leaflets\n    * Setting average bulk water region of PMF to zero\n    * Symmetrizing PMF (for symmetrization by anti-symmetrization of weighted gradients see [`symmetrize_profile.py`](analysis/permeability/symmetrize_profile.py))\n    * Computing error by deviation from unsymmetrized PMF\n    * Calculating pKa shift profile given two PMFs\n* See examples located [here](analysis/permeability/examples/)\n* The scripts for ABF are more up-to-date than the umbrella sampling ones, though all should be fully functional.\n* 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.\n    * I did NOT write this script; it is from the SI of ref. 4.\n    * The code here was extracted from the SI PDF, reformatted with proper spacing (fixing artifacts of copy/paste), and documentation was added.\n\n\n## Directory tree\n\n```\n.\n├── ABF\n│   ├── 01_prep\n│   │   └── plain_abf_files\n│   ├── job_scripts\n│   └── winmerge\n├── analysis\n│   ├── 01_area-box-lipid\n│   ├── 02_density-profile\n│   │   └── example\n│   ├── 03_permeant-position\n│   └── permeability\n│       ├── archive\n│       └── examples\n│           ├── abf_pmf_processor\n│           ├── calc_perme\n│           └── matchX\n├── US\n│   ├── 01_setup\n│   ├── 02_analysis\n│   │   ├── 01_area\n│   │   ├── 02_overlap\n│   │   ├── 03_wham\n│   │   └── 04_mbar\n│   └── diffusivity\n│       ├── 1_fromSI\n│       └── 2_fblockavg\n└── waterbox\n\n27 directories\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fvtlim%2Fpermeability","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fvtlim%2Fpermeability","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fvtlim%2Fpermeability/lists"}