ECC-lipids

ECC-lipids is a classical MD lipid force field with an implicit embedding of the electronic polarization through the Electronic Continuum Correction (ECC).

Electronic polarization (included e.g. via ECC) is important for accurate interactions of charged molecules, cation and anions, like sodium or divalent calcium cations, as well as for overall neutral molecules like zwitterionic lipids, e.g. POPC.

All interaction parameters of ECC-lipids are based on Amber Lipid14 (POPC, POPE) or Lipid17 (POPS, POPG) force fields.

This work is open to any contribution from anyone from pointig out bugs, raising issues improving this page and adding extra starting structures, to adding new molecules and headgroup-tail combinations and improving the whole force field.

Enjoy ECC-lipids, fork this repository and contribute through pull requests!

Quick start

Good news - using ECC-lipids in your simulations is easy! All ECC-lipids topologies are available at ecc_lipids/topologies/ecc-lipids/.

The ECC-lipids topology files are created for two popular naming conventions:

• CHARMM-compatible naming convention
• AMBER-compatible naming convention

The difference between them is only in the order of atoms and their names in coordinate and topology files. Importantly, the interaction parameters are identical and simulations with either of the two conventions yield the same configuration ensembles.

Starting configurations

Several equilibrated starting configurations are available below for both naming conventions.

CHARMM-compatible topologies and configurations

Several starting structures:

• POPC bilayer (SPC/E water, 4 CaCl2, equilibrated)
• POPS bilayer (SPC/E water, ECC-ions NaCl counterions, equilibrated)
• POPC:POPS (10:1) bilayer (SPC/E water, ECC-ions NaCl counterions, equilibrated)
• POPC:POPS (1:1) bilayer (SPC/E water, ECC-ions NaCl counterions, equilibrated)
• POPC:POPS (4:1) bilayer (SPC/E water, ECC-ions NaCl counterions, equilibrated)
• POPC:POPS (5:1) bilayer (SPC/E water, ECC-ions NaCl counterions, equilibrated)
• POPC:POPS (5:1) bilayer (SPC/E water, ECC-ions KCl counterions, equilibrated)

Zenodo deposits including more details, e.g. long trajectories, salt concentrations, tested water models, simulation settings … :

• POPC and POPS lipid bilayers (various mixtures) and Na+ (K+) counterions - Zenodo deposit
• POPC and POPS lipid bilayers (various mixtures) and Na+ (K+) counterions and additional CaCl2 concentrations - Zenodo deposit

Can use CHARMM-gui!

Also, since the molecular topology of ECC-lipids is designed to agree with CHARMM lipids, ECC-lipids can be used directly with the membrane structures generated by CHARMM-gui after only changing the provided topology files (GROMACS format). An example topology for ECC-lipids is given in topologies/ecc-lipids.

Amber Lipid14-compatible topologies and configurations

• POPC bilayer without ions and 3-point water model (SPC/E)
• POPC bilayer without ions and 4-point water model (TIP4p-2005)
• Simulations of POPC lipid bilayer in water solution at various NaCl and CaCl2 concentrations - Zenodo deposit with SPC/E water model
• Simulations of POPC lipid bilayer in water solution at various NaCl and CaCl2 concentrations - Zenodo deposit with various water models

If you require Amber-like topology, you can use AmberTools to make bilayers for Lipid14 and use the ECC-lipidds topology with the Amber-like conventions, e.g. Amber-like ECC-POPC. The difference between the Amber-like resp. CHARMM-like topologies are only in the atomic naming and ordering conventions, and they generate identical results.

Databases with configurations and trajectories

Already equilibrated structures from various force fields including CHARMM and Amber Lipid14/17 can be also downloaded from the lipid membrane simulation database generated by the NMRlipids project, and also by searching Zenodo.

Which water model?

This is always a tricky question. For ECC-lipids, we have chosen the SPC/E water model as the standard 3-site water model, and TIP5p/2005 as the standard 4-site water model, as these are consistent with the principles underling ECC. However, the results with ECC-lipids are robust with respect to the choice of the water model as is shown in SI of ECC-POPC publication.

Which simulation software?

Simulations with ECC-lipids were mostly performed with GROMACS, but were also tested with openMM as is shown in SI of ECC-POPC publication.

Papers with ECC-lipids

• Accurate Binding of Sodium and Calcium to a POPC Bilayer by Effective Inclusion of Electronic Polarization, ECC-POPC also available at GitHub
• Improved Cation Binding to Lipid Bilayers with Negatively Charged POPS by Effective Inclusion of Electronic Polarization ECC-POPS also available at GitHub
• Simulation of processes in cellular membranes PhD thesis including POPC, POPE and POPS; also on GitHub

Related work

• NMRLipids projects
  • Molecular electrometer and binding of cations to phospholipid bilayers, also on GitHub
  • Headgroup Structure and Cation Binding in Phosphatidylserine Lipid Bilayers, also on GitHub

• Charge scaling manifesto

• Accurate Biomolecular Simulations Account for Electronic Polarization

• Molecular dynamics in electronic continuum (MDEC)
  • MDEC 2009, Electronic continuum model for molecular dynamics simulations
  • MDEC 2010, Electronic Continuum Model for Molecular Dynamics Simulations of Biological Molecules

Notes

The directory structure and working style of this repository is highly inspired by open-collaboration NMRLipids projects, with its GitHub repositories.

Repository MATCH is often also employed as a data source and a tool with analysis scripts.

Gromacs compatible parameters for ECC-ions (and many other ions) are maintained at a separate repository.