Amber 14 and Amber 14 Tools released
Version 14 of the Amber software suite has been released (There was no "unlucky" Amber13.)
- Force fields: Amber has two new fixed-charge protein force fields, ff14SB and ff14ipq, a new modular lipid force field, Lipid14, and updates to nucleic acid and carbohydrate force fields.
- Improved options for self-guided Langevin dynamics and accelerated molecular dynamics, to enchance sampling along soft degrees of freedom.
- A completely reorganized Reference Manual
- QM/MM calculations can interface with a variety of external quantum chemistry programs, expanding the types of quantum models available
- More features from sander have been added to pmemd for both CPU and GPU platforms, including performance improvements, and support for extra points, multi-dimension replica exchange, a Monte Carlo barostat, ScaledMD, Jarzynski sampling, explicit solvent constant pH, GBSA, and hydrogen mass repartitioning. Support is also included for the latest Kepler, Titan and GTX7xx GPUs.
- Expanded methods are available for free energy calculations that change Hamiltonian models, including better procedures for appearing and disappearing atoms, and tighter integration with replica-exchange simulations, and a new absolute free energy method.
- New facilities are present for using electron density maps (e.g. from cryo EM/ET experiments) as constraints, and to support rigid (or partially flexible) groups in simulations.
Amber Tools have also been updated.
Among the new features in AmberTools14:
- The sander module, our workhorse simulation program, is now a part of AmberTools;
- Greatly expanded and improved cpptraj program for analyzing trajectories;
- new documentation and tools for inspecting and modifying Amber parameter files;
- Improved workflow for setting up and analyzing simulations;
- new capability for semi-empirical Born-Oppenheimer molecular dynamics;
- EMIL: a new absolute free energy method using TI;
- New Free Energy Workflow (FEW) tool automates free energy calculations (LIE, TI, and MM/PBSA-type calculations);
- Completely reorganized Reference Manual