flip-flops

Simple program for calculating the number of flip-flop events in Gromacs simulations.

Fast implementation of the lipid orientation method from Li et al., 2024.

Installation

0. Install Rust.

1. Clone this repository:

$ git clone https://github.com/Ladme/flip-flops.git

2. Navigate to the repository.

3. Build the program using cargo:

$ cargo build --release

A binary file named flip-flops will be built inside target/release/.

Usage

Calculate number of flip-flop events.

Usage: flip-flops [OPTIONS] --structure <STRUCTURE> --tails <TAILS>

Options:
  -s, --structure <STRUCTURE>
          Path to a gro, pdb, or tpr file containing the system structure.

  -f, --trajectory <TRAJECTORIES>...
          Path to the xtc file(s) containing the trajectory to be analyzed.

  -n, --index <INDEX>
          Path to an ndx file containing groups associated with the system.

  -o, --output <OUTPUT>
          Path to an output file where the detected flip-flops are to be written. If not provided, the output is written to stdout.

      --heads <HEADS>
          Groan selection language query selecting atoms representing lipid heads. There should only be one selected atom per lipid molecule.
          
          [default: "name PO4 P"]

      --tails <TAILS>
          Groan selection language query selecting atoms representing ends of lipid tails.

  -b, --begin <BEGIN>
          Time of the first frame to read from the trajectory (in ps). All previous frames will be skipped.
          
          [default: 0.0]

  -e, --end <END>
          Time of the last frame to read from the trajectory (in ps). All following frames will be skipped.
          
          [default: NaN]

  -s, --step <STEP>
          Analyze only every <STEP>th frame of the input trajectory.
          
          [default: 1]

      --transition <TRANSITION>
          Angle range that defines the transition zone between the upper and lower leaflets. Lipids whose orientation angle falls within this zone are treated as belonging to neither leaflet.
          
          [default: "55.0 125.0"]

      --window <WINDOW>
          Number of neighboring frames on each side of the current frame to include in the sliding window for running average of the lipid angle. The window spans 2N+1 frames in total. Set to 0 to disable smoothing.
          
          [default: 0]

  -h, --help
          Print help (see a summary with '-h')

  -V, --version
          Print version

Limitations

This program has a lot of limitations. The most important ones include:

• the membrane is assumed to be planar and built in the xy plane,
• each lipid molecule is assumed to be composed of a single residue,
• simulation box is expected to be orthogonal.