Amber12 Bug Fixes
12.0 March, 2012
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 AmberTools 13 manual
in Chapter 1 Section 5. See
Jason's wiki page for more detailed instructions, as well as a work-around in
case you are behind a firewall that blocks update_amber from contacting
If you wish to apply these updates, run the command
As a note, the Amber configure script automatically checks for and downloads
Fix issue where restart files from pmemd can be truncated upon abnormal
termination of pmemd.
This updates the version number of all Amber programs (sander, pmemd, and
addles) to report Amber 12.
This turns EMAP reading errors into fatal errors and fixes restart file printing
for pmemd minimizations (completing bugfix.1)
Prevents potential user errors with the QM/MM interface to external QM
packages if the QM region has a charge. Also included are missing
test files for mechanical embedding.
Fix to prevent compilation and linking errors on sander.PUPIL program.
- bugfix.6: Sometimes the temperature
was not set from the ASCII restart file when restarting a T-REMD simulation.
- bugfix.7: Fix bugfix.1 so you don't
get errors opening the restart file if you don't use "-O" on the command-line.
- bugfix.8: Remove an optimization directive
that causes sporadic softcore-TI run SHAKE errors with some compilers.
- bugfix.9.bz2_: Large CUDA upgrade patch.
This is a major update to the GPU support in AMBER 12 and also contains
minor bug fixes for the CPU version of pmemd.
- Support for Kepler K10 and GTX6XX GPUs
- New, high-performance, lower-memory footprint hybrid fixed precision model: SPFP
- Support for REMD using 1 GPU per replica
- Various bugfixes and tweaks for aMD, IPS, GB and NMR restrained simulations
- bugfix.10: Multiple bugfixes for regular and softcore TI.
- bugfix.11: Update to bugfix.10,
for the net charge removal code.
- bugfix.12: Fix race condition in pmemd.cuda.MPI
that may cause failures in parallel GPU simulations.
- bugfix.13: Fix the instability problem of H-REMD trajectories (both sander and pmemd)
by swapping velocities as well as coordinates. updating test/h_rem and test/cnstph_remd appropriately.
- bugfix.14: Multiple fixes and
updates for GPU code:
- Adds support for CUDA Toolkit 5.0
- Fixes bugs in the Jarzynski code on GPUs and re-enables it.
- Fixes a bug with the use of harmonic restraints when running with NPT.
- Enables GBSA simulations in GPU runs.
- Updates requested citations.
- Fixes uninitialized variables in NMRopt=1 runs that could cause crashes
with some compilers.
- Adds check for forgetting to specify gamma_ln with ntb>1 and ntt=3
- Updates GPU code to v.12.2
- bugfix.15: Fixes for QM/MM Ewald:
- add self-plasma term for charged systems
- improve default values for k space vectors
- corresponding updates to tests
- bugfix.16: Update sander/PBSA tests
to the results from AmberTools version 13.
- bugfix.17: Update a sander/PBSA
test for update.4 to AmberTools 13.
- bugfix.18.bz2: Fixes a number of
issues with pmemd and pmemd.cuda:
- Updates GPU code to v12.3
- Adds check to prevent running ntb=2 with gamma_ln=0
and ntt=3 or 4.
- Fixes Hamiltonian Replica Exchange on GPUs and CPUs in explicit solvent.
- Fixes issue with nmropt DUMPAVE printing in pmemd for H-REMD.
- Fixes extra-points support for the GLYCAM force field which
was leading to a segfault in pmemd and pmemd.cuda.
- Improves stability for NPT simulations on GPUs.
- Adds check to make sure code quits if skinnb would go negative
in GPU calculations due to large reductions in box size.
- Fixes issues with restart of NPT simulations on GPUs in cases
where the box size had shrunk considerably.
- Fixes minimizations on GPUs with the SPFP precision model by
truncating large forces that occur during the beginning of a
- Changes pmemd.cuda and pmemd.cuda.MPI links to be relative
instead of absolute in AMBERHOME/bin directory.
- Updates configure script to optimize for sm35 GPU hardware
(Kepler II) in cases where cuda v5.0 is detected.
- Makes GTX680 output the gold standard for test cases.
- Fixes incorrect timings that were reported at the end of a run
with REMD runs in pmemd.
- bugfix.19: Minor updates
- Adds support for CUDA 5.5. - via accompanying AMBERTools 13 bugfix.16.
- Disables NMROPT on multiple GPUs due to unfixed bugs in the MPI version
- Enables support for GTX-Titan and GTX780 GPUs and checks that the minimum
required driver version of v325.15 is installed.
- Fix spurious crash with kNLBuildNeighborListOrthogonal16_kernel
for systems containing large vacuum bubbles or very low density.
- Updates GPU code citation.
- Adds missing test case output for GPU Jarinski Tests.
- Updates GPU code to v12.3.1
- bugfix.20: Allow pmemd.cuda to
run with CUDA driver version 319.60 or older.
- bugfix.21: EXTERN QM/MM enhancements and bug fixes:
- For Orca:
- Fix bug with forces on MM atoms (update read format for Orca .pcgrad files)
- Fix problems with parallel Orca runs
- Enable single point trajectory post-processing
- Update dipole moment output to Debye
- For Gaussian:
- QM/MM with MP2 and electrostatic embedding now uses MP2 density to compute correct MP2 forces on MM atoms
- Allow 256 character route section (avoids truncation)
- Fix problems with Gaussian 03
- For ADF:
- Update dipole moment ouput to Debye
- For all:
- Template input files support 256 characters per line (avoids truncation)
- Input of charge and spin multiplicity in the namelist of the external
- QM program has been deprecated - this needs to be given in the &qmmm
namelist (variables qmcharge and spin)
- Includes updates to tests