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Amber is a molecular dynamics (MD) software package first conceived by Peter Kollman, his lab and collaborators to simulate biomolecular systems. The pmemd module is available as a serial version for central processing units (CPUs), NVIDIA and Advanced Micro Devices (AMD) graphics processing unit (GPU) versions as well as Message Passing Interface (MPI) parallel versions. Advanced capabilities include thermodynamic integration, replica exchange MD and accelerated MD methods. A brief update to the software and recently added capabilities is described in this Application Note. 

Abstract FORMOSAT-3/COSMIC (F3/C) constellation of six micro-satellites was launched into the circular low-earth orbit at 800 km altitude with a 72-degree inclination angle on 15 April 2006, uniformly monitoring the ionosphere by the GPS (Global Positioning System) Radio Occultation (RO). Each F3/C satellite is equipped with a TIP (Tiny Ionospheric Photometer) observing 135.6 nm emissions and a TBB (Tri-Band Beacon) for conducting ionospheric tomography. More than 2000 RO profiles per day for the first time allows us globally studying three-dimensional ionospheric electron density structures and formation mechanisms of the equatorial ionization anomaly, middle-latitude trough, Weddell/Okhotsk Sea anomaly, etc. In addition, several new findings, such as plasma caves, plasma depletion bays, etc., have been reported. F3/C electron density profiles together with ground-based GPS total electron contents can be used to monitor, nowcast, and forecast ionospheric space weather. The S4 index of GPS signal scintillations recorded by F3/C is useful for ionospheric irregularities monitoring as well as for positioning, navigation, and communication applications. F3/C was officially decommissioned on 1 May 2020 and replaced by FORMOSAT-7/COSMIC-2 (F7/C2). F7/C2 constellation of six small satellites was launched into the circular low-Earth orbit at 550 km altitude with a 24-degree inclination angle on 25 June 2019. F7/C2 carries an advanced TGRS (Tri Gnss (global navigation satellite system) Radio occultation System) instrument, which tracks more than 4000 RO profiles per day. Each F7/C2 satellite also has a RFB (Radio Reference Beacon) on board for ionospheric tomography and an IVM (Ion Velocity Meter) for measuring ion temperature, velocity, and density. F7/C2 TGRS, IVM, and RFB shall continue to expand the F3/C success in the ionospheric space weather forecasting.