Data

Tools

Indexes

Applications

Experiments

Open Source Science

Recent Releases of https://github.com/choderalab/yank

https://github.com/choderalab/yank - 0.25.2 - Bugfix release

Bugfixes

  • Fixed a bug that causes YANK to crash in when thermodynamic trailblazing is interrupted and then resumed with the option bidirectional_redistribution set (#1195).

- Python
Published by andrrizzi over 6 years ago

https://github.com/choderalab/yank - 0.25.1 - Bugfix and more robust yank status command

Bugfixes

  • The command yank status now handles gracefully the case where it attempts to open a locked netcdf file (#855).
  • Fix bug causing YANK to crash sometimes when the option bidirectional_redistribution was activated (#1192).

- Python
Published by andrrizzi over 6 years ago

https://github.com/choderalab/yank - 0.25.0 - Moved multistate and mpi modules and new trailblaze algorithm

API-breaking changes

  • The yank.mpi module and the objects in the yank.multistate package, which were deprecated in 0.24.0, have now been removed, and they can be found in the mpiplus and openmmtools libraries respectively.
  • The function yank.pipeline.trailblaze_alchemical_protocol has been renamed yank.pipeline.run_thermodynamic_trailblazing (#1180).

New features

  • The thermodynamic trailblazing algorithm used for the authomatic generation of the alchemical path is now capable of resuming after an unexpected interruption or crash. The samples generated during the process are used to initialize the replicas of the replica exchange or SAMS free energy calculation. This behavior can be controlled through the start_from_trailblaze_samples YAML option (#1176, #1180).
  • It is possible to control more options of the thermodynamic trailblazing algorithm and to discretize an alchemical path given through mathematical expressions enslaved to a generic variable (#1180).
  • Added a --setup-only flag in the yank script CLI command to run the automatic setup pipeline without running the free energy calculation (#1178).

Bugfixes

  • Fix a bug in which a list of experiments: [exp1, exp2] in the YAML file containing an unknown experiment name would fail silently without error (#1178).
  • Fixed a problem that would prevent YANK to work with Cerberus >= 1.2 (#1180).
  • Fixed the error message displayed when the anisotropic dispersion correction cutoff was too big for the box dimension (#1181).

Enhancements

  • By default, the automatic determination of the alchemical path now starts with the harmonic/flat-bottom restraint turned off and activate it in intermediate states instead of keeping the restraint activated throughout the calculation and reweighting in the analysis stage (#1176).

Known issues

  • Using parallel MPI processes causes poor mixing of the odd thermodynamic states while the mixing of the even states is normal. We're still investigating whether the issue is caused by a change in the MPI library or an internal bug. For now, we recommend running calculations using only 1 GPU (choderalab/openmmtools#449 and #1130).
  • Simulations restored from a checkpoint file have their velocities reset to zero (#1115).
  • Forward and backward convergence analysis free energy traces in the Jupter notebook are incorrect (#971).
  • Setup will fail if .mol2 atom substructure ID matches filename (#703).

- Python
Published by andrrizzi over 6 years ago

https://github.com/choderalab/yank - 0.24.1 - Bugfix release

Bugfixes

  • Fixed import of logsumexp() which was moved from scipy.misc to scipy.special (#1162).
  • Fixed a bug in which validation of molecules and system file paths did not consider paths relative to the YAML script path (#1164).
  • Improve the robustness of opening the netcdf file on resuming of the multi-state samplers by setting the environment variable HDF5_USE_FILE_LOCKING to 'FALSE' after 4 failed attempts (#1168).
  • Fixed a bug causing a crash during exception handling (#1168).
  • Fixed a bug causing a crash in selftest.py when loading OpenEye (#1170).

Enhancements

  • The class yank.utils.TLeap can now create octahedral boxes. This is not exposed in the YAML script yet, however (#1160).

- Python
Published by andrrizzi about 7 years ago

https://github.com/choderalab/yank - 0.24.0 - Experimental support for online status files

  • Added an experimental feature that allows --status to be provided with yank script invocations to emit a status.pkl file in the experiment directory at the conclusion of each experiment switch interval (#1135). This feature is experimental, and its invocation may be changed in a future release.
  • This release requires OpenMMTools >= 0.17.0, which includes a much faster way of implementing exact treatment of PME during alchemical calculations (#1136).
  • Some NetCDF robustness improvements.
  • SAMS improvements:
    • SAMS now properly restores t0 and stage, which should correctly persist the stage across phase switches and resumes.
    • Added SAMS logZ_history plot to notebook reports.
    • SAMS self._stage is now an integer to more easily store this in storage (0 is initial, 1 is asymptotic phase).
    • Suppress some verbose outputs.
    • If an asymptotically optimal stage is present in a SAMS simulation, the initial stage is discarded to equilibration and automatic equilibration detection is applied to the asymptotically optimal weight adjustment region only.
    • Jupyter notebook reports now show SAMS weight convergence if present.
  • The yank.multistate package was deprecated. In the future, this package will be available in OpenMMTools (#1146).

Known issues

  • The use of more than one process per experiment via MPI has known issues that are being debugged (#1130).
  • Simulations restored from a checkpoint file have their velocities reset to zero (#1115).
  • Forward and backward convergence analysis free energy traces in the Jupter notebook are incorrect (#971).
  • Peptide ligands are not currently supported (#376).
  • Setup will fail if .mol2 atom substructure ID matches filename (#703).

- Python
Published by andrrizzi over 7 years ago

https://github.com/choderalab/yank - 0.23.7 - Bugfix release

Fix bug where resuming a simulation caused the checkpoint iteration to crash (#1103).

- Python
Published by andrrizzi almost 8 years ago

https://github.com/choderalab/yank - 0.23.6 - Bugfix release

  • Fix bug where redefining MCDisplacement/RotationMove in the YAML mcmc_moves block without specifying atom_subset caused the MC move to affect the whole system instead of only the ligand atoms (#1099).
  • Add net_charge option to the antechamber YAML pipeline for charged small molecules (#1099).
  • Added YAML syntax tutorial in the online documentation (#1099).

- Python
Published by andrrizzi almost 8 years ago

https://github.com/choderalab/yank - 0.23.5 - Bugfix release

  • Fix bug where the stack trace of an exception raised by an MPI process would be logged incorrectly (#1084).
  • Improved robustness of NetCDF dataset opening and closing (#1084).
  • The algorithm identifying ions now detects also ions called "NA" and "CL" (#1086).
  • Fix bug that caused the standard state correction of Boresch restraints to be computed incorrectly (#1092).

- Python
Published by andrrizzi almost 8 years ago

https://github.com/choderalab/yank - 0.23.4 - Bugfix release

  • Fix bug #1012 when determining automatically the group_size of replica exchange simulations with MPI (#1073).
  • Fix bug where passing WT to the modeller directive caused the automatic setup pipeline to crash (#1074).

- Python
Published by andrrizzi almost 8 years ago

https://github.com/choderalab/yank - 0.23.3 Adds support for single mutations using Modeller

  • Adds an optional modeller directive to the molecules section of the YAML file through Modeller, a tool for comparative modeling of protein structures.
  • The following options are accessible through the modellerdirective. (docs)
    • apply_mutations: Specify protein single mutations (e.g., T315I). (docs)
  • Multi-analyze feature can now create directories for multi-report output instead of raising an error.

- Python
Published by Lnaden almost 8 years ago

https://github.com/choderalab/yank - 0.23.2 - More Multi-Experiment Cleanup

  • resume_setup and resume_experiment are True by default
  • Fixed bug where yank analyze extract-trajectory could not be executed
  • Further updated multi-analysis docs to reflect multi-experiment changes

- Python
Published by Lnaden almost 8 years ago

https://github.com/choderalab/yank - 0.23.1 - Multi-Experiment and Online Bug

  • Fixed bug in MultiExperimentAnalyzer where a path ending in the folder separator (e.g. /) caused all files to write to the same place.
  • Fixed bug where increasing number of iterations did not continue experiment if online analysis was turned on and previously hit the max number of iterations
  • Fixed bug where online analysis and harmonic unbiasing caused MBAR to not form due to misformed initialfk
  • MultiExperimentAnalyzer now gracefully traps an error caught by one experiment without crashing others Fixed bug in MultiStateReporter when there were unsampled thermodynamic states as end-states but they referenced sampled thermodynamic states for their standard system

- Python
Published by Lnaden about 8 years ago

https://github.com/choderalab/yank - 0.23.0 Multi-Analysis

Analysis can now be parallelized through MPI and targeting a YAML file which generated a YANK experiment.

Features

  • Added new ExperimentAnalyzer class as API call for auto_analyze like functions. Supports serialized output to Pickle
  • Added new MultiExperimentAnalyzer class to analyze all experiments found in a YAML input file with the ExperimentAnalyzer. Supported by MPI for parallel action
  • Unified all auto_analyze like objects to go through the ExperimentAnalyzer, such as the API and Jupyter Notebook calls
  • Existing API calls should remain unchanged and serve as pass-throughs to the new classes
  • Major changes to the CLI behavior of yank analyze and yank analyze report to support the new features. These should not affect existing code, only support new features.

Bug fixes

  • Fixed bug in yank selftest with the OpenEye tests. Also silenced the OpenEye internal tests due to time. Dependency checks are still active

Improvements

  • Update API docs

- Python
Published by Lnaden about 8 years ago

https://github.com/choderalab/yank - 0.22.3 Balance Checkpoint with IO

  • Reduced default checkpoint interval to 50 (was 200) to balance disk IO time with time between checkpoints.
  • Fixed bug in DSL selection string from YAML

- Python
Published by Lnaden about 8 years ago

https://github.com/choderalab/yank - 0.22.2 - Topography Property Copy

  • Critical bug fix for Topology where ions of charged ligands were considered part of the ligand with respect to restraints.
  • Online analysis MBAR failures can no longer halt simulations
  • Added ability for analyze CLI (--fulltraj) and API (use_full_trajectory=True) to force use the full trajectory

- Python
Published by Lnaden about 8 years ago

https://github.com/choderalab/yank - 0.22.1 - Online Analysis Default

  • Online analysis will always run by default now, with no target error, run every checkpoint interval, and with at least 200 iterations
  • Online analysis can now be a set to the checkpoint interval by setting online_analysis_interval: "checkpoint" in the YAML files (application layer, not API)
  • Checkpoint interval increased from default of 10 to 200
  • Analysis now uses the online-analysis data if available by default

- Python
Published by Lnaden about 8 years ago

https://github.com/choderalab/yank - 0.22.0 RMSD the Casbah

Enhancements and features

  • Added RMSD Type restraint, requires OpenMM 7.3 or greater to access. You can have older versions of OpenMM, but this feature is unavailable and will raise a graceful error should you attempt to use it.
  • Added more robust last good iteration saving
  • Added more robust restore from checkpoint access
  • Exposed checkpoint interval iterations in MultiStateReporter
  • Generalized the Boresch restraints to a BoreschLike restraint to support new energy functions.
  • Boresch restraint automatic atom selection now picks bonded heavy atoms
  • Boresch restraints no longer accept standardstatecorrection_method as an option
  • Added new Haversined Torsion Boresch Torsion (PeriodicTorsionBoresch) Boresch-like restraint where functional form of torsion is periodic support more numerically stable energy functions
  • Changed the timeseries analysis to only consider a maximum number of points on which to evaluate "is this equilibrium" to speed up process.
  • Implement #848 Use MDTraj Trajectory.save() method instead of inferring function from extension.
  • Implement #635 Allow extract-trajectory to handle trajectories with 1 frame.

Bugfixes

  • Fix bug #941 where unbiasing the restraint would crash the analysis if using a 32-bit OpenCL platform.
  • Fix bug #945 where relative imports of OpenEye tools would cause problems on some systems.
  • Temporarily pinned NetCDF4 to 1.3.1 until we can fix the bug introduced in 1.4.0 where masked arrays are always returned. This pin will be lifted in future releases.
  • Fix a bug where maxniterations was ignored when computing the mixing statistics of the calculation (PR #963).
  • Fix bug #944 where ReplicaExchange.create() did not accept a single SamplerState anymore.
  • Fix a bug where the box vectors of SamplerStates were initialized incorrectly in MultiStateSampler.create() for NVT calculations (PR #969).
  • Fix bug #964 where using the state index argument in extract_trajectory with SAMS calculations would cause a crash.

Backwards compatibility breaks

  • Boresch Standard State Correction no longer has an analytical correction

- Python
Published by Lnaden about 8 years ago

https://github.com/choderalab/yank - 0.21.2 - More Post-Sams Bugfixes

  • Fix analysis on 32-bit platforms OS agnostic (#942).
  • More robust analysis tests (#942).
  • Pin Cerberus to 1.1 as 1.2 breaks some schemas (#952). Proper fix in a later version.
  • UML Diagrams added to docs (#953).
  • Fix API bug for resuming simulations without specifying how many iterations to run (#955).

- Python
Published by Lnaden about 8 years ago

https://github.com/choderalab/yank - 0.21.1 - Post-SAMS Bugfixes

  • Fix bug in FIRE minimizer logging (#932).
  • Fix Cray environment variables (#932).
  • Make tests more robust to undersampled analysis results (#932,#934,#936).
  • Fix molecule imaging incorrectly in trajectory extraction (#933).

- Python
Published by Lnaden over 8 years ago

https://github.com/choderalab/yank - 0.21.0 SAMS and General Multistate Samplers

This release represents a major change in the YANK code base

Summary of Release

YANK's sampling scheme now has a generalized scheme and runs on one of four primary samplers:

  • MultiStateSampler: Fixed state sampler where no states mix
  • ReplicaExchange: Dense state sampling with state swapping each iteration
  • ParallelTempering: Special extension of ReplicaExchange which swaps temperatures, with more efficient energy evaluation
  • SAMSSampler: Self-Adjusted Mixture Sampling. Single replica sampler which dynamically samples all thermodynamic states with long enough run time

The samplers are now part of the YANK multistate module and will eventually be ported to OpenMMTools. The YAML syntax has been extended that two new sections can be specified: MCMC Moves, and Samplers. These are fully optional blocks which default to a specific set if not specified. Several old YAML options like number_of_iterations have been moved to the samplers block and replaced with default_X where X is the old setting name.

The old scheme of the single repex.py file housing all sampler and reporter information has been removed and the entire multistate module is designed to be extended and experimented with. Similarly, much of the old analyze.py module has been migrated to multistate and can be extended as well.

Detailed Changes

  • Generalize the Sampler framework into a new multistate module and generalized sampler class structure
  • Analysis suite now general and part of multistate with additional YANK-specific extensions in YANK's analyze.py module
  • Analysis energies have been converted from old u_kln format to u_kn formalism
  • Test suites for samplers refactored to be general and test all samplers
  • Test suites for analysis refactored to be general and test all samplers
  • Samplers now operate on concept of neighborhood to determine which thermodynamic states the energy of a sample was evaluated at
  • Cleaned up language in "replica" (sampler), "state" (thermodynamic state), and "sample" (drawn from replica)
  • Improved online analysis in samplers with general I/O functions in reporter
  • Python notebooks now can serialize their data
  • Added notebook feature to do a free energy trace trying to converge free energies by progressively truncating more data from front and back
  • Restraint factories improved and redundant code cleaned up
  • Generalized utilities for checking function calls
  • Improved storage read speeds by chunking HDF5 data to use the checkpoint interval for per-iteration instead of each iteration
  • Dependencies now defined purely by Conda meta.yaml and no longer through setup.py. pip can no longer check for dependencies because of this
  • Added ability to unbias harmonic restraints during analysis
  • mcmc block added to the YAML syntax
  • samplers block added to the YAML syntax
  • Improved resuming boot up times by requiring newer OpenMMTools features
  • Renamed global option number_of_iterations to default_number_of_iterations.
  • Renamed global option timestep to default_timestep.
  • Renamed global option nstepsperiteration to defaultnstepsper_iteration. (docs)
  • The global options collisionrate, `mcdisplacementsigma, andintegrationsplittingare not supported anymore, but they can still be specified in themcmc_moves` block.
  • Added support for automatic determination of processes_per_experiment (now the default).
  • Simulation minimization tries FIRE Minimizer first before falling back to L-BFGS.
  • Fixed bug in Boresch restraints where atoms were not correctly re-randomized when initial pick is numerically unstable

Release Code Name: SAMSon and Delilah

- Python
Published by Lnaden over 8 years ago

https://github.com/choderalab/yank - 0.20.1 - Exact treatment of PME electrostatics and optimizations

  • Allow users to specify options for openmmtools.alchemy.AbsoluteAlchemicalFactory in the YAML file. In particular, this introduces exact treatment of PME electrostatics for charged ligands. (#881)
  • Major optimization of the computation of the energy matrix. (#881)
  • Added the YAML option max_n_contexts. (#881)
  • Bumped minimum required version of openmmtools to 0.14.0.

- Python
Published by andrrizzi over 8 years ago

https://github.com/choderalab/yank - 0.20.0 - Support for processing proteins through PDBFixer

- Python
Published by Lnaden over 8 years ago

https://github.com/choderalab/yank - 0.19.4 - Schema and Parallel Setup Fixes

  • Fixed bug in parallel molecule setup which caused the same molecule to be setup multiple times (#850).
  • Fixed bug in Cerberus schema for LEaP where molecule parameters accumulated (#847).
  • Fixed bug where options in experiment section were not coerced (#853).
  • Fixed status command to print information about all combinatorial experiments (#853).
  • Faster restart with combinatorial experiments (#853).

- Python
Published by Lnaden over 8 years ago

https://github.com/choderalab/yank - YANK 0.19.3 - Support for Amber restart files

  • Added support for Amber rst7 files in phase1_path/phase2_path (#840).
  • The CLI option jobid now uses 1-based numbering like Torque and LSF do for array jobs (#840).

- Python
Published by andrrizzi over 8 years ago

https://github.com/choderalab/yank - YANK 0.19.2 - Include ions in the solute-only trajectory

Ions are now included in the solute-only trajectories (#835).

- Python
Published by andrrizzi over 8 years ago

https://github.com/choderalab/yank - 0.19.1 Trailblaze fix and restart stability from OpenMMTools

  • OpenMMTools 0.13.4 now required to fix issues listed below
  • Restrained atoms to absolute coordinates caused issue in Trailblaze with a Barostat
  • Last restart attempt uses a slower, but more robust restart method

- Python
Published by Lnaden over 8 years ago

https://github.com/choderalab/yank - Regions, Cerberus, and Errors

New Features

  • Added statistical inefficiency of replica state indices to the analysis (#819).
  • Improve automatically generate residue names for sdf and SMILES molecules (#819).
  • Improved automatic parameterization for FlatBottom restraint. An error is now raised if the restraint volume is greater than the periodic box volume (#797 ).
  • Added custom region selection to Topography, including compound regions
  • Custom regions can now be defined through YAML
  • Restraints atom selection in restraints can now use Topography Regions
  • Topography now can select from arbitrary string, either complex regions, DSL strings, and in the future SMARTS strings

Cerberus

  • Changed to Cerberus for data validation (was Schema), public facing validation schemas in the future

This requirement and package change modifies the way that YAML files are validated and returns a much more complete, and detailed description of the errors in your sections. This should drastically reduce the confusion around "What went wrong with my YAML file"

Critical Bugfixes

OpenMMTools 0.13.3 now required to fix bug in SamplerState

Minor Bugfixes

  • Fixed a bug where setup logs were saved in the wrong folder (#819).
  • Fixed a bug that caused FlatBottom/Harmonic restraints to crash when only a single atom was selected (#819).
  • Fixed a bug in extract-trajectory that was causing the trajectory to not be imaged properly (#819).
  • Implemented work-around that avoid tleap problems with numerical unit names (#819).
  • Added better error handling of known LEaP Errors
  • Fixed issue for startframe and endframe were ignored for trajectory extraction
  • Better MPI exception handling
  • Fixed bug where one MPI thread crashing did not stop other threads, resulting in them getting stuck in a blocking action, but not dying.

- Python
Published by Lnaden over 8 years ago

https://github.com/choderalab/yank - Python 2 Dropped, Solute Only Trajectories, and Trailblaze Bug fixes

Dependency changes

  • Python 2.X Support officially removed - YANK now runs Python 3.5 and 3.6 only

Features Added by this Release

  • Added GAFF2 Torsion support based on YAML input files
  • Solute-only trajectories can now be stored every iteration, regardless of checkpoint interval

Improvements in this release

  • Added restraint selection flowchart to documentation
  • Use infinity instead of None to specify unlimited number of iterations (#772).
  • Parallelized setup of molecules and systems with MPI (#557)
  • Generalized restrained atoms selection during trailblaze scheme to include non-protein receptors (see also choderalab/openmmtools#290).

Notable Bugfixes

  • Fix loading of leap parameters from a local .dat files (allow us to use local versions of gaff parameters for validation)
  • Trailblaze protocol crashes with MPI (#762).
  • Fixed bug when computing reduced potentials of simulated energies during trailblaze scheme.
  • Automatic path is saved in YAML as a mix of python and numpy floats (#763)
  • Fixed the number of neutralizing counterions when receptor and ligand have opposite charges (we were adding too many in this case).
  • Fixed the log file name with lists of experiments that ended up being just .log.
  • Implemented workaround for fixing the net charge of cyclic multi-residue mol2 files.

- Python
Published by Lnaden almost 9 years ago

https://github.com/choderalab/yank - Auto Alchemical Path, Split Langevin Integrators, and More

Features added by this release

  • Automatic Alchemical Path Determination (#726)
  • Langevin Splitting Integrator which allows custom sub-division of a timestep for more accurate simulations (#747)
  • Online Free Energy Analysis with simulation stop criteria of target error in free energy difference (#712)
  • Jupyter Notebooks can now be pre-rendered as static HTML or PDF files, PDF requires LaTeX (#740)
  • Experiments can be parallelized by splitting MPI communicator (#726)

Improvements added by this release

  • Centroids for restraints now selectable through DSL string instead of whole molecule
  • Ionic Strength ability added to setup pipeline
  • Website fully documented, all pages filled in
  • API fully documented on website and auto-generated from docstrings
  • YAML pages on website should be much easier to read

Notable Bugs Fixed

  • Removed Ligand rotation/displacement attempts with Boresch restraints to improve replica exchange
  • Analyze module fully tested, related bugs found and corrected

Notable Refactoring and Dependency changes

  • YAMLBuilder class and yamlbuilder.py file refactored ExperimentBuilder and experiment.py respectively
  • Anisotropic Dispersion correction options reduced to a single setting
  • Added MDTraj, Jupyer, and Matplotlib as dependencies
  • Updated OpenMMTools dependency minimum version to 0.13.0

- Python
Published by Lnaden almost 9 years ago

https://github.com/choderalab/yank - 0.16.2 Startup Speed and Reduced File Sizes

This release helps reduce the initial file sizes of your analysis files by compressing the objects to recreate the alchemical systems. This gives over 10x reduction in the initial file sizes, and saves minutes off the initial start up before simulations start.

  • Automatic Expanded Cutoff Distance Selection
  • Compressed stored systems drastically reduce initial file sizes
    • Requires OpenMMTools 0.11.2, minimum version updated
  • Use C Yaml Dumper and Loaders to speed up YAML object processing

- Python
Published by Lnaden about 9 years ago

https://github.com/choderalab/yank - 0.16.1 Auto Expanded Cutoffs and bug fixes for Transition Matrix and Reporter

  • Expanded cutoff now able to be chosen automatically instead of just hard coded number
  • Restraint parameters can now be specified in the YAML file which pass to restraints API
  • Fixes bug causing transition matrix to be computed incorrectly, uses empirical to estimate
  • Allows user to drop samples equilibration report to avoid plot scale being dominated by initial fast equilibration

- Python
Published by Lnaden about 9 years ago

https://github.com/choderalab/yank - 0.16.0 Full API and Python 3.6

  • Full feature API for setting up, running, and analyzing experiments
  • Supports new generalized MCMC moves, ThermodynamicStates, and other features from improved OpenMMTools
  • Checkpoint feature added to reduce file size, add portability to data analysis files.
  • Simulations can now alternate between phases to allow analysis even before simulations are done
  • OpenEye features compartmentalized so you don't need every OpenEye feature YANK could use to use any of them
  • Major under the hood speed ups to base code and MPI behavior, includes a full code refactor.
  • Mol2 files can now read in multi-molecule files
  • No longer uses standalone Alchemy module, uses the one built into OpenMMTools
  • Added Python 3.6 support.
  • Retired Python 3.4 support

- Python
Published by Lnaden about 9 years ago

https://github.com/choderalab/yank - 0.15.2 Health Report and Anisotropic Dispersion Control

  • Added simulation Health Report through a Jupyter Notebook with CLI support
  • Added ability to control Anisotropic Dispersion Correction through YAML files

- Python
Published by Lnaden over 9 years ago

https://github.com/choderalab/yank - 0.15.0 Backend and Helpful Debugging Build

  • Added support for solvent_dsl in user defined systems of YAML pages
  • Removed Command Line Interface ability to do yank prepare and yank run
  • Added ability to overwrite individual YAML commands from command line
  • Added YAML feature to extend_simulation without modifying YAML files or command line every iteration
  • NaN's generated during simulations serialize system, state, and integrator which can be passed off for debugging to others
  • Backend website updating and pushes improved
  • Improved GROMACS extension file handling

- Python
Published by Lnaden over 9 years ago

https://github.com/choderalab/yank - YANK 0.14.1: Early Access 1.0 Release

This release marks the early access phase for YANK 1.0. We intend for this to be a formal release for users to test YANK and its functionality while we refactor the underlying Python API.

In this release: - YAML Syntax Structure Frozen. YANK YAML Version 1.0. All YAML scripts from this version will be compatible with future versions until YAML 2.0 New features may appear in the time meantime, but scripts will be forwards compatible. - Initial support for OpenMM XML systems and PDB files - Support for separate solvent configurations for the two phases when defined from amber/gromacs/openmm files - clearance in YAML no mandatory parameter of explicit solvent, but only when molecule setup goes through pipeline - Boresch Orientational Restraints fully implemented and documented. - Long range anisotropic dispersion correction improved to work on both ends of thermodynamic cycle leg - Documentation updated with better algorithms and theory sections. - Full walkthroughs of yank-examples added to online documentation - Various other documentation improvements - Support for upcoming OpenMM 7.1 Release and features (still works with 7.0.1) - YANK now on MIT License - Many bugfixes

Validation

YANK has been validated for binding against T4-Lysozyme with the binders: Benzene, Ethylbenzene, Isobutylbenzene, and Indene with the FF14SB Amber Force Field. Our binding free energies match those in the following paper within error:

David L. Mobley, Alan P. Graves, John D. Chodera, Andrea C. McReynolds, Brian K. Shoichet, and Ken A. Dill. Predicting absolute ligand binding free energies to a simple model site. J. Mol. Biol. 371:1118, 2007. [DOI]

We have also validated YANK hydration free energies against a reduced set in the FreeSolv Database in TIP3P water based on construction from SMILES strings. The molecular list can be found here. The paper we compared against can be found here:

David L. Mobley and J. Peter Guthrie. FreeSolv: a database of experimental and calculated hydration free energies, with input files. J. Comp.-Aided Mol. Design 28:7, 2014 [DOI]

- Python
Published by Lnaden over 9 years ago

https://github.com/choderalab/yank - YANK 0.12.0 Split Examples Release

This release splits out the examples from the main YANK repo and starts depreciating tests and functions in preparation for the removal of much of the CLI functions.

- Python
Published by Lnaden over 9 years ago

https://github.com/choderalab/yank - YANK 0.11.2

This version adds better long range dispersion and electrostatic corrections.

Even better documentation to YAML files, including some best practices guidelines.

- Python
Published by Lnaden almost 10 years ago

https://github.com/choderalab/yank - YANK 0.11.0 Full YAML Documentation

YANK's YAML documentation has been fully written and published.

Due to the scope of this documentation, and the level of options it provides the users, a full release has been cut.

Documentation on how to propose and publish updates have also been added.

- Python
Published by Lnaden almost 10 years ago

https://github.com/choderalab/yank - 0.10.0

This release enables Python 3.X compatibility for YANK. - Python 3.4 and Python 3.5 are now supported - Online documentation has been updated to include the YAML input files - Selftests now provide more helpful output

- Python
Published by Lnaden almost 10 years ago

https://github.com/choderalab/yank - 0.9.0

In this release: - Changed YAML syntax. - New command yank analyze extract-trajectory to extract data from NetCDF4 file in a common trajectory format. - Support for solvation free energy calculations. - Automatic detection of MPI. - Various bug fixes.

- Python
Published by andrrizzi almost 10 years ago

https://github.com/choderalab/yank - 0.8.0

This release incorporates numerous revisions and bugfixes: - Alchemical functionality is now encapsulated in a separate module called alchemy - Support for YAML-based specification of calculations has been added. This uses an AmberTools-based pipeline under the hood. - Lots of bugfixes

- Python
Published by jchodera about 10 years ago

https://github.com/choderalab/yank - Alchemical Hamiltonian replica exchange overhaul

This version features a complete overhaul of how alchemical Hamiltonian replica exchange is implemented. Now, a single Context object is used for all alchemical states, and only the context parameters are updated for each state. Startup should be much faster and the simulations should run more efficiently.

- Python
Published by jchodera almost 11 years ago

https://github.com/choderalab/yank - Last revision before alchemical repex overhaul

This is the last revision before alchemical repex overhaul to give major speedup.

- Python
Published by jchodera about 11 years ago

https://github.com/choderalab/yank - 0.6.2

Temporary pre-release for tutorial session and testing various upstream dependencies.

- Python
Published by kyleabeauchamp about 11 years ago

https://github.com/choderalab/yank - Adds mpi4py dependency to conda recipe

- Python
Published by jchodera over 11 years ago

https://github.com/choderalab/yank - 0.6

- Python
Published by kyleabeauchamp over 11 years ago

https://github.com/choderalab/yank - Partially stable development release (in use by some collaborators)

This version is being frozen as a release because it is in use by several collaborators, including the Geerke lab.

- Python
Published by jchodera almost 12 years ago