You give isolf a lipid recipe, and it writes the coordinates. With --top or --inp it also writes the topology and force-field files GENESIS reads. Lipids use the iSoLF implicit-solvent model, so there's no water to add. It's a single binary, with nothing else to install.
Install · Quick start · Build modes · Examples · Output · Run in GENESIS · License
macOS / Linux
curl -LsSf https://raw.githubusercontent.com/bondrewd/isolf/main/install.sh | shWindows (PowerShell)
powershell -ExecutionPolicy ByPass -c "irm https://raw.githubusercontent.com/bondrewd/isolf/main/install.ps1 | iex"The installer picks the right binary for your machine, checks its sha256, drops it in ~/.local/bin, and puts that on your PATH. Update in place with isolf update. Remove it with isolf uninstall.
Other ways to install
# with wget instead of curl
wget -qO- https://raw.githubusercontent.com/bondrewd/isolf/main/install.sh | sh
# pin a version, or change the install directory
curl -LsSf https://raw.githubusercontent.com/bondrewd/isolf/main/install.sh | sh -s -- 0.1.0
curl -LsSf https://raw.githubusercontent.com/bondrewd/isolf/main/install.sh | ISOLF_INSTALL_DIR=/usr/local/bin sh
# from source, with a Rust toolchain (https://rustup.rs)
cargo install --path .You can also download a prebuilt binary from the Releases page. Pick windows-msvc.zip, apple-darwin.tar.gz, or one of the *-linux-musl.tar.gz files, unzip it, and run ./isolf --version. On macOS, clear the quarantine flag once with xattr -dr com.apple.quarantine ./isolf.
isolf --upper POPC=1 --lipids-per-leaflet 256 --top --out my_first_membraneThis writes my_first_membrane/ with the structure (membrane.gro), the topology (membrane.top), and the lipid force field (isolf.itp). Add --inp for a full GENESIS setup, or --vmd for a viewer script.
The flags you pass choose one of 2 modes:
| Mode | Example |
|---|---|
| Membrane | isolf --upper POPC=1 --lipids-per-leaflet 256 --out m |
| Vesicle | isolf --upper POPC=1 --vesicle 20 --out v |
Lipids are NAME=WEIGHT recipes like "POPC=3,POPS=1" (repeat --upper/--lower or comma-separate to combine). A name has 4 letters, <tails><head>, and there are 35 in all. Set a different bottom leaflet with --lower. Size a membrane by lipid count or --membrane (e.g. x=10,y=20); size a vesicle by --vesicle (ro=20, ri=15, or both).
While it runs, isolf prints each phase and a closing summary: the composition, the box, the particle count, the time, and the command to run next. Use -q for the summary alone, -v for every file path, --ascii for plain glyphs.
🧪 More recipes are in EXAMPLES.md: asymmetric leaflets, rectangular and box-sized membranes, vesicles, and the output formats.
Everything lands in the --out folder. The .gro structure and a .log run log are always written. The rest are opt-in:
| Flag | Adds |
|---|---|
--top |
the topology (.top) and the force-field include (isolf.itp) |
--inp |
GENESIS control files for a 3-step run (implies --top) |
--vmd |
a VMD script (and the .psf it loads) to view the structure |
--gif |
a GIF animating the leaflet relaxation |
--pdb --psf --crd --cif |
extra coordinate and structure formats |
The full file table and the reproducible run log are in EXAMPLES.md → Output files.
Run the control files in order. Each one continues from the previous step's restart:
atdyn min.inp # 1. minimization
atdyn npt.inp # 2. equilibration (nvt.inp for a vesicle)
atdyn pro.inp # 3. productionEvery option, grouped by topic with its default, is in isolf --help.
Thanks to Hideto Tsubouchi for testing the code.
Licensed under either of Apache-2.0 or MIT, at your option. Any contribution you submit is dual licensed as above, unless you say otherwise.
Disclosure: This codebase was built with the help of a coding AI from my Python and Julia scripts, and is currently maintained by humans 🧑🔬 and ai 🤖.