Noteworthy Changes In Amber 14
The following is an incomplete list of the changes and improvements implemented
in Amber and AmberTools since their previous releases (Amber 12 in 2012 and
AmberTools 13 in 2013).
- Improved workflow for setting up and analyzing simulations
- Greatly expanded cpptraj functionality, including support for
the Grid Inhomogenous Solvent Theory (GIST)
- New capability for semi-empirical Born-Oppenheimer molecular dynamics
- A new method to compute absolute free energy changes using a
thermodynamic integration scheme (EMIL)
- Multi-dimensional Replica Exchange molecular dynamics in sander,
pmemd, and pmemd.cuda.
- Improved performance for pmemd.cuda and vastly improved parallel
performance and scaling, using peer-to-peer communications when
- Completely reorganized Reference Manual
- Implementation of scaled Molecular Dynamics in sander and
- QM/MM calculations can have adaptive quantum regions
- Adaptive buffered force-mixing QM/MM calculations can be run
- Constant pH molecular dynamics is now supported in implicit and
explicit solvent in both sander and pmemd.
- Constant pH replica exchange molecular dynamics has been implemented in
both sander and pmemd.
- Improved tool for analyzing constant pH simulations
- Hydrogen mass repartitioning is supported via ParmEd.
- Support for chamber-style topology files with
- ParmEd can run MD calculations on GPUs using OpenMM
- New divalent metal ion parameters and a new 12-6-4 Lennard-Jones
potential is available for use in sander and pmemd.
- Molecular Dynamics can be run using 3D-RISM in sander.
- Force trajectories can now be written.
- EMAP and SGLD are now implemented in pmemd.
- Linear least-squares dihedral term fitting in paramfit.
- Update bundled NetCDF to NetCDF version 4.
- New analysis tools for crystal lattice simulations.
- New environment resource scripts to help set up shell environment
- Improved support of CHARMM force fields and VMD-generated topology
files using chamber.