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Amber Bug Fixes and Updates

Note: The individual bug fixes for Amber are described below in case you want to see what they do, or apply patches by hand. Most users are encouraged to use the update_amber script (which is automatically run during the cmake 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 Reference Manual in Chapter 2, Section 4, or just go to your amber20_src directory and type

./update_amber --help

If you wish to apply the listed Amber updates, run cmake again.

Amber20 Updates (April, 2020)

  • update.1: Fix CpHMD problem in

    pmemd.cuda.MPI

    .
  • update.2: Improve performance of

    pmemd.cuda

    on Turing GPUs.
  • update.3: Update the way Plumed handles truncated octahedral boundary conditions.
  • update.4: Change RAMD code in

    pmemd

    to avoid bias in the direction selection.
  • update.5: Several fixes to

    pmemd

    and

    pmemd.cuda

    related to TI and REMD
  • update.6: Update

    pmemd

    to the latest version of plumed.
  • update.7: Fix MBAR printout in

    pmemd.MPI

  • update.8: Fix CMAP memory allocation in

    pmemd.cuda

  • update.9: Fixes a bug in LiGaMD & Pep-GaMD in

    pmemd.cuda

  • update.10: Updates

    pmemd

    to support gfortran10
  • update.11: Second update to

    pmemd

    to support gfortran10

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.
  • update.3: This update fixes the following:
    1. Corrects REMD error trap for different box sizes in

      pmemd

      to account for non-periodic systems.
    2. Bugfix in

      pmemd

      to properly restart MultiD-REMD simulations with two or more pH, redox potential or temperature dimensions.
  • update.4: Major update to

    pmemd.cuda

    , fixing various bugs. See the GPU Patches page for a full description.
  • update.5: Adds support for MC and Berendsen barostats in order to run the benchmark suite in the midpoint code. Additionally improves dynamic memory allocation.
  • update.6: Fix rare non-reproducibility issue in

    pmemd.cuda

    .
  • update.7: Fix in

    pmemd.cuda

    Fixes a memory usage issue when using center of mass restraints.
  • update.8: Fix and extend the NFE capabilities in

    pmemd

    .
  • update.9: Re-allow the functionality of backbone restraints/water restraints when running GTI simulations in

    pmemd.cuda

    .
  • update.10: Adds a new speed optimized mcwat code that allows for the simulation of water exchange in buried binding sites in

    pmemd.cuda and pmemd

    .
  • update.11: Minor tweak to update.10 to allow compilation using Intel compilers.

  • update.12: Performance updates for

    pmemd.cuda

    running on Volta or Turing GPUs and using CUDA10.
  • update.13: Fixes for center of mass restraints in

    pmemd.cuda

    . Also minor variable declaration updates for reproduction of mcwat results.
  • update.14: Put a copy of AmberNetcdf.F90 into the

    pmemd

    source code tree, allowing it to be different than the one used in AmberTools.
  • update.15: Update NEB capability in

    pmemd.cuda.MPI

    .
  • update.16: Modifies the way softcore free energy calculations are done in

    pmemd

    ; more info.
  • update.17: Add files needed to implement the ff19SB protein force field.

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.
  • update.15: Corrects REMD error trap for different box sizes in

    pmemd

    to account for non-periodic systems.
  • 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 newer releases of AmberTools.

"How's that for maxed out?"

Last modified: Apr 29, 2021