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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
  2. (eABF) Smoothed Biasing Forces Yield Unbiased Free Energies with the Extended-System Adaptive Biasing Force Method
  3. (meta-eABF) Zooming across the Free-Energy Landscape: Shaving Barriers, and Flooding Valleys
  4. (ABF vs. US) Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds
  5. NAMD user guide for version 2.13

Notes

  • There is a Python module here called 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)
    • Computing error by deviation from unsymmetrized PMF
    • Calculating pKa shift profile given two PMFs
  • See examples located here
  • 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 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