Software available from BBS

Cardioid.  Cardiac multiscale simulation suite.  Cardioid spans simulations from subcellular mechanisms to organ-level clinical phenomena. The suite contains tools for simulating cardiac electrophysiology, cardiac mechanics, torso-ECGs, cardiac meshing, and fiber generation.

ConveyorLC.  High Performance Computing software for parallel docking and MM/GBSA rescoring.  Massively parallel (15,000+ cpus) implementation of AutoDock Vina and Amber.

ddcMD. Domain-decomposition molecular dynamics.  A fully GPU-accelerated update of LLNL's molecular dynamics program implemented for the Martini force field.

ddcMDconverter. Python tool to convert GROMACS files to ddcMD inputs.

MDAnalysis for ddcMD. Modified version of MDAnalysis to support ddcMD.

ezAlign.  Coarse-grain to atomistic molecular coordinate and topology converter for molecular dynamics simulations.

Maestro workflow management.  Maestro is an open-source HPC software tool that defines a YAML-based study specification for defining multistep workflows and automates execution of software flows on HPC resources. 

MemSurfer.  Membrane surface analysis.  Software to compute and analyze membrane surfaces found in a wide variety of large-scale molecular simulations. MemSurfer works directly on the 3D point coordinates independently of the type of simulation, and can handle a variety of membranes as well as atomistic and coarse-grain simulations. MemSurfer provides many analysis tools, such as computing membrane curvature, lipid density, lipid normals, and area per lipid. MemSurfer provides a Python API that can be used/extended to perform other types of analyses.

MuMMI Multiscale machine-learned modeling infrastructure framework.  The MuMMI framework facilitates the coordination of massively parallel multiscale simulations.  MuMMI was developed as part of the Pilot2 project of the Joint Design of Advanced Computing Solutions for Cancer funded jointly by the Department of Energy and the National Cancer Institute.

DynIm.  Dynamic importance sampling.  Python package -- used within MuMMI -- to sample high-dimensional data sets.  DynIm minimizes redundancy and maximizes the coverage of sampled points. DynIm uses the notion of "dissimilarity" from previously-selected samples to define the importance of potential selections, and selects samples that are most dissimilar. DynIm provides a farthest-point sampling approach.

MuMMI-RAS.  Application component of the MuMMI framework developed to create large-scale ML-driven multiscale simulation ensembles to study the interactions of lipid plasma membranes with RAS proteins ("Rat sarcoma;" mutations to these proteins are implicated in 30% of human cancers) and RAS-RAF protein complexes (part of the growth signaling pathway).

Pytaridx.  Python interface for reading and appending tar files, while keeping a fast index for finding and reading files in the archive.  This interface stored and managed over one billion files in a Pilot2 simulation campaign using MuMMI.