High-Throughput Automated Preparation and Simulation of Membrane Proteins with HTMD

HTMD
is a programmable scientific platform intended to facilitate
simulation-based research in molecular systems. This paper presents
the functionalities of HTMD for the preparation of a molecular dynamics
simulation starting from PDB structures, building the system using
well-known force fields, and applying standardized protocols for running
the simulations. We demonstrate the framework’s flexibility
for high-throughput molecular simulations by applying a preparation,
building, and simulation protocol with multiple force-fields on all
of the seven hundred eukaryotic membrane proteins resolved to-date
from the orientation of proteins in membranes (OPM) database. All
of the systems are available on www.playmolecule.org.