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Amber Bug Fixes and Updates

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 reason. Most 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 trouble-shooting easier.

Instructions for using update_amber can be found in the Amber 2018 Reference Manual in Chapter 2, Section 3. See Jason's wiki page for more detailed instructions. Note that update_amber has built-in Proxy support (see the Amber Reference Manual for instructions on setting up your Proxy).

If you wish to apply these updates, run the command

$AMBERHOME/update_amber --update

Alternatively, the Amber configure script automatically checks for and downloads updates so you can just recompile Amber.

Amber18 Updates (April, 2018)

  • update.1: Adds an error message to

    pmemd

    when users run REMD and the box sizes are not the same across all replicas.
  • update.2: Fix in

    pmemd

    the neighbor pairs inside the pH and redox potential dimensions on multidimensional REMD simulations.

Amber16 Updates (April, 2016)

  • update.1: Adds GPU support for including external electric fields.
  • update.2: Completes GPU support for including external electric fields.
  • update.3: Adds support for Intel Xeon and Intel Xeon Phi Optimizations.
  • update.4: New free energy routines in

    pmemd

    ; see nfe.pdf for full documentation.
  • update.5: Support Titan-XP in AMBER 16 pmemd.cuda.
  • update.6: Provides a 10 to 15 percent performance boost to GP102,104 and 107 based gpus, which include GTX-1060,1070,1080, Titan-XP, Quadro P5000 and P6000. Also enables execution on P100 based GPUs.
  • update.7: Updates printouts in the code (re SM60) to match those on the gpu page of the web page.
  • update.8: Fix NetCDF restart writing for

    pmemd

    when internal coordinate axes are flipped.
  • update.9: Fixes and extensions to the "nfe" options in

    pmemd

    .
  • update.10: Fix vulnerability that allowed Lennard-Jones 12-6-4 potentials to be applied with incompatible features in

    pmemd

    .
  • update.11: Fixes overwriting output in gamd.log when continuing a simulation.

    pmemd

    .
  • update.12: Fixes dt and nstep passing in gpu force calculations (primarily used in oscillating electric fields).

    pmemd,sander

    .
  • update.13: Fix for

    pmemd.cuda

    to trap simulations with small periodic cells that can lead to incorrect pair lists.
  • update.14: Adds an error message to

    pmemd

    when users run REMD and the box sizes are not the same across all replicas.

Amber14 Updates (April, 2014)

  • update.1: Fixes a bug in

    pmemd.amoeba.MPI

    when running on multiple processors as well as a small fix in the

    pmemd.amoeba

    softcore code.
  • update.2: 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.
  • update.3: 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.
  • update.4: Fixes incorrect printing of Ewald Error Estimate for CPU based

    pmemd

    runs.
  • update.5: 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.
  • update.6: Updates GPU code to v14.0.1 - add support for CUDA 6.5, fixes issues on > 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.
  • update.7: 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.8: Update code to use 80 character line width to fix compile issues with certain compilers.
  • update.9: Enhancements have been made to the MIC offload implementation for improved performance. Please refer to the documentation for more details.
  • update.10: 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.
  • update.11: Updates and bug fixes in pmemd.cuda relating to emap, COM restraints and the GB solvent model:
    1. emap: A check has been added to prevent restraints when using emap as they are not yet supported on the GPU.
    2. 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.
    3. GB: Fixes undocumented uninitialized variable in DPFP GB simulations that was causing inconsistent results.
  • update.12: Updates test cases for the new GBneck2 nucleic acid parameters introduced with AmberTools 15. This should make sure that all Amber14 tests pass after upgrading.
  • update.13: 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.

Amber12 Updates (March, 2012)

  • bugfix.1: Fix issue where restart files from pmemd can be truncated upon abnormal termination of

    pmemd

    .
  • bugfix.2: This updates the version number of all Amber programs (

    sander

    ,

    pmemd

    , and

    addles

    ) to report Amber 12.
  • bugfix.3: This turns EMAP reading errors into fatal errors and fixes restart file printing for pmemd minimizations (completing bugfix.1)
  • bugfix.4: 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.
  • bugfix.5: 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.
    1. Support for Kepler K10 and GTX6XX GPUs
    2. New, high-performance, lower-memory footprint hybrid fixed precision model: SPFP
    3. Support for REMD using 1 GPU per replica
    4. 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:
    1. Adds support for CUDA Toolkit 5.0
    2. Fixes bugs in the Jarzynski code on GPUs and re-enables it.
    3. Fixes a bug with the use of harmonic restraints when running with NPT.
    4. Enables GBSA simulations in GPU runs.
    5. Updates requested citations.
    6. Fixes uninitialized variables in NMRopt = 1 runs that could cause crashes with some compilers.
    7. Adds check for forgetting to specify gamma_ln with ntb>1 and ntt=3 .or. 4
    8. Updates GPU code to v.12.2
  • bugfix.15: Fixes for QM/MM Ewald:
    1. Add self-plasma term for charged systems
    2. Improve default values for k space vectors
    3. Corresponding updates to tests
  • bugfix.19: Minor updates to

    pmemd.cuda

    :
    1. Adds support for CUDA 5.5. - via accompanying AMBERTools 13 bugfix.16.
    2. Disables NMROPT on multiple GPUs due to unfixed bugs in the MPI version at present.
    3. Enables support for GTX-Titan and GTX780 GPUs and checks that the minimum required driver version of v325.15 is installed.
    4. Fix spurious crash with kNLBuildNeighborListOrthogonal16_kernel for systems containing large vacuum bubbles or very low density.
    5. Updates GPU code citation.
    6. Adds missing test case output for GPU Jarinski Tests.
    7. 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:
      1. Fix bug with forces on MM atoms (update read format for Orca .pcgrad files)
      2. Fix problems with parallel Orca runs
      3. Enable single point trajectory post-processing
      4. Update dipole moment output to Debye
    • For Gaussian:
      1. QM/MM with MP2 and electrostatic embedding now uses MP2 density to compute correct MP2 forces on MM atoms
      2. Allow 256 character route section (avoids truncation)
      3. Fix problems with Gaussian 03
    • For ADF:
      1. Update dipole moment ouput to Debye
    • For all:
      1. Template input files support 256 characters per line (avoids truncation)
      2. Input of charge and spin multiplicity in the namelist of the external
      3. QM program has been deprecated - this needs to be given in the &qmmm namelist (variables qmcharge and spin)
      4. Includes updates to tests
  • Older versions of Amber are no longer supported for bug fixes. If you are using one of these versions, all of the functionality that you might have gotten through the

    sander

    program or auxiliary software are now distributed freely with much never releases of AmberTools.

"Insert clever motto here."

Last modified: Jun 5, 2018