1.8 Building Membrane Systems - Overview
Building Membrane Systems is tricky in Amber. A force field for the each molecule type including each lipid component must be chosen. Various members of the Amber community have developed tutorials, which are listed here. Common methods to build a membrane system include using:
Lipid Force Fields
Please see the force fields page to learn about Lipid Force Fields.
Tools and Tutorials to Build Membrane Systems
CHARMM-GUI Setup
By Wonpil Im
Some people find it easier to set up a system for simulation in Amber using the CHARMM-GUI interface. These tutorials were written by Wonpil Im at Lehigh University. He also has You Tube videos on these tutorials.
Building Systems with CHARMM-GUI
PACKMOL-Memgen
By Stephan Schott Verdugo
This tutorial will show you alternative ways of building a membrane system to perform molecular dynamics simulations within Amber, with or without an embedded protein, and with the optional inclusion of ligands. This is not a trivial task, as membrane environments are anisotropic (i.e. they are not the same in every dimension of the system), and, compared to typical explicit water simulations, the initial condition is important to obtain a representative structure in a reasonable simulation time.
Using PACKMOL-Memgen to Setup and Run a Membrane Simulation-updated 2023
PACKMOL-Memgen
By JD Callum
PACKMOL-Memgen is built into Amber.
This tutorial uses the CCG MOE GUI for protein preparation (add hydrogens, cap termini, set protonation states). You may have access to MOE or a similar GUI/tool to achieve the same task. PACKMOL-Memgen also has prep options.
Lipi21 and PACKMOL-Memgen Setup
An Amber Membrane Simulation Tutorial: Lipid14
By Benjamin D. Madej and Ross C. Walker
This tutorial explains how to set up and
simulate lipid bilayers with the Lipid14 force field and CHARMM-GUI.
This is a more general tutorial that walks you through how to build a system, equilibrate it, run MD and monitor properties.
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