Ultra-Small Vesicle Simulations (AA · MARTINI · DPD)

Multiscale modeling of lipid vesicles across all-atom (AA), MARTINI, and DPD resolutions. This repository provides minimal, reproducible examples with all required inputs (topologies/parameters), reference logs, and ready-to-use run scripts for GROMACS and LAMMPS.

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For more information

These scripts were implemented in the paper:

"Structural and Dynamical Consistency in Vesicles across All-Atom, MARTINI, and Dissipative Particle Dynamics" by Wandi Xu, Xingfei Wei, Gene Chong, Udaya Dahal, Qiang Cui, and Rigoberto Hernandez.

A URL to the paper will appear here when it is available.

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Installation

Clone this repository to your local machine:

git clone https://github.com/rxhernandez/USUV.git
cd USUV

Contents

• DPD/

  • in.* / in.480vesiclewater_5 — LAMMPS input scripts
  • pair.settings, group.settings — force/pair and group settings
  • production.run.lmps — example batch/run script
  • equilibration.state — equilibrated state / restart
  • log.lammps — reference run log

• MARTINI/

  • *.gro, *.top, *.itp — GROMACS structures and topologies
  • index.ndx — index file
  • step6.6_equilibration.gro — equilibration snapshot
  • step7_production.log — production log
  • lipidtail_posres.pdb — example position restraints (if applicable)

• AA/

  • 480vesiclewater_5_all.xyz, data.480vesiclewater_4, data.480vesiclewater_4.zip — example systems
  • log.lammps — top-level reference log

Requirements

• LAMMPS (for DPD examples)
• GROMACS ≥ 2021.4 (for MARTINI examples)
• MPI toolchain (optional, for parallel/HPC runs)
• Job scheduler (e.g., Slurm) (optional, for batch scripts)

On clusters, load the appropriate modules (e.g., module load gromacs/2021.4, module load lammps, module load openmpi) and adjust partition/nodes/cores in the provided scripts.