14.0 April, 2014
Note: The individual bug fixes are described below in case you want to
see what they do, or you don't want to use update_amber for some
users are encouraged to use the update_amber script (which is in
$AMBERHOME, and is automatically
run during the configure step) to handle patching tasks. This
script automatically downloads and applies patches on this site individually and
keeps track of every patch that has been applied, making patching and
Instructions for using update_amber can be found in the Amber 14 manual
in Chapter 2 Section 1. See
Jason's wiki page for more detailed instructions.
If you wish to apply these updates, run the command
Alternatively, the Amber configure script automatically checks for and downloads
updates so you can just recompile Amber.
Fixes a bug in pmemd.amoeba.MPI when running on multiple processors as
well as a small fix in the pmemd.amoeba softcore code.
Fixes a bug in pmemd.MPI when running with constant pressure
ntp = 1, barostat = 1 (default) and a large number of processors.
This bug causes a deviation in the pressure calculation.
Presence of this bug can be identified when running under
constant pressure and block_fft = 1 appears in the output file.
Fixes printout of NMRopt trace variables (distances, angles, torsions,
etc.) when using the Monte Carlo barostat in pmemd. Also prevents illegal
values of mcbarint with multiple time-stepping integrators.
Fixes incorrect printing of Ewald Error Estimate for CPU based PMEMD runs.
Adds MIC offload support to pmemd. This update enables use of Intel Xeon Phi co-processor cards in offload mode where the card acts as an accelerator for the direct space sum.
Updates GPU code to v14.0.1 - add support for CUDA 6.5, fixes issues on .gt. 4 gpus, enables peer to peer support on 8 gpus for systems that support it in hardware and adds checks for NANs in restrt files.
Fixes a bug in that would cause the number of shake constraints removed to be reported incorrectly with softcore TI. Add an additional warning if shake is attempted for bonds that have large differences in equilibirum bond lengths.
Update code to use 80 character line width to fix compile issues with certain compilers.
Enhancements have been made to the MIC offload implementation for improved performance.
Please refer to the documentation for more details.
Center of mass distance restraints now supported in the GPU engine.
Usage follows the same setup and protocol as in the CPU implemetation. For the GPU implementation all calculations including COM are done on the GPU.
Updates and bug fixes in pmemd.cuda relating to emap, COM restraints and the GB solvent model:
- emap: A check has been added to prevent restraints when using emap as
they are not yet supported on the GPU.
- COM restraints: The number of atoms in a COM grouping has been increased from 200 to 1024.
A bug has been fixed that was preventing distance restraints from correctly being
detected when the restrain involved atom 1.
- GB: Fixes undocumented uninitialized variable in DPFP GB simulations that was causing
Updates test cases for the new GBneck2 nucleic acid parameters introduced
with AmberTools 15. This should make sure that all Amber14 tests pass
Fixes GPU-COM distance restraint bug in pmemd.cuda.
Adds error checking code to catch ir6 = 1 when used with GPU-COM distance restraints.
Improves the GPU-COM distance restraint test cases.