MemSurfer is an efficient and versatile tool to compute and analyze membrane surfaces found in a wide variety of large-scale molecular simulations. MemSurfer works independently of the type of simulation, directly on the 3D point coordinates, and can handle a variety of membranes as well as atomic simulations. MemSurfer provides many built-in analysis tasks, such as computing the membrane curvature, density and normals of lipids, and area per lipid. More importantly, MemSurfer provides a simple-to-use Python API that researchers can easily use/extend to perform other types of analysis.
MemSurfer is an analysis tool that predates the Joint Design of Advanced Computing Solutions for Cancer (JDACS4C) pilot projects, but Pilot 2 improved and optimized it. Researchers use MemSurfer to perform basic analysis of membrane simulations (such as local area densities) in preparation for creating a macro model from coarse-grained molecular dynamics data.
Researchers who want to compute and analyze membrane surfaces or study their properties for large computational jobs such as those carried out by the JDACS4C Pilot 2 program.
Requires many software dependencies, even on well-supported high-performance computing systems such as NIH's Biowulf.
MemSurfer allows analysis of membranes that are highly complex and have curved geometries that greatly deviate from a simple planar state, appropriately characterizing the geometric and topological properties of the membrane surface. It works independently of the type of simulation and directly on 3D point coordinates; as a result, MemSurfer can handle a variety of membranes. MemSurfer provides direct access to the membrane surface itself, allowing the user to potentially conceive and compute a variety of nonstandard properties.
To use the software contained in this GitHub repository, choose one of the following options:
- If you want to use MemSurfer without installation, you can access the Preinstalled MemSurfer on Biowulf.
- If you want to modify the code for your purposes, you can (very carefully) install a copy of MemSurfer and external dependencies using MemSurfer Installation on Biowulf, based on instructions from Lawrence Livermore National Laboratory (LLNL).
The example directory includes a simple example to test the installation and to demonstrate the functionality of MemSurfer. (The MemSurfer Installation on Biowulf also contains a section on testing the installation process.) The example reads a point set that represents a 2D sinusoidal surface with added noise in z-dimension and generates *.vtp files that you can visualize using Paraview.
LLNL released MemSurfer under GNU GPL-3.0 license.
For details, refer to LICENSE and NOTICE.
LLNL-CODE-763493
Authors: Harsh Bhatia (hbhatia@llnl.gov) and Peer-Timo Bremer
Released: July 22, 2021