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future

Placeholder for issues to address in a not-yet-decided/not-yet-planned future release

8%

177 issues   (13 closed — 164 open)

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Bug

4/26
Feature

4/67
Task

5/84
Related issues
Bug #716: Memory leak in g_rms when using the -prev flag
Bug #1117: ensemble-averaged distance restraints is probably broken
Bug #1166: g_order is incorrect for unsaturated carbons
Bug #1235: peptide dihedral angle definitions violate IUPAC
Bug #1339: Center of mass drift with Nose-Hoover, MTTK and md-vv
Bug #1476: Odd behavior with verlet-buffer-drift
Bug #1730: gmx compare does not compare all fields of a .tpr
Bug #1827: cmake multi-configuration generator support partly broken
Bug #1839: pdb2gmx: Failure to rename non-standard hydrogen atom names after generating missing hydrogens in pdb2gmx
Bug #1880: PP-PME load balancing issue
Bug #1919: static linking issues cause by hwloc support
Bug #2044: X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group
Bug #2211: gmx writes normal output to stderr
Bug #2360: error at counter reset with PME-only rank
Bug #2421: EwaldUnitTests and SimdUnitTests fail on ppc64le with gcc-8.0.1
Bug #2468: incorrect GPU timing reported with OpenCL and domain decomposition
Bug #2483: gmx dump writes mdp files that can not be parsed by grompp
Bug #2544: gmx rmsf does not fix periodicity in reference structure
Bug #2568: gmx editconf -rotate does not rotate the box
Bug #2598: Tools using read_next_x cannot read TNG files with sanitzers
Bug #2649: Virial calculation necessary for correct energy calculation on GPU
Bug #2693: Several memory leaks in mdrun
Bug #2734: regressiontests/kernel core dumps on ppc64le
Bug #2763: GMXAPI layout / grouping in development docs "modules" page
Bug #3049: gmx nmeig should plot a real infrared spectrum
Bug #3368: Erroneous interplay between gmx rms command and atommass.dat: Can not find mass in database for atom MG in residue
Feature #438: New tool: g_correl
Feature #720: permit pdb2gmx to choose a kind of HIS based on proton position
Feature #742: Enhancing the performance of the free energy code
Feature #760: Implement rigid body groups
Feature #889: pressure annealing
Feature #895: g_rmsf previous frame as reference
Feature #907: Add tests for verifying installed headers
Feature #951: Multiple versions of Gromacs (e.g., single and double) in the same library/binary
Feature #1053: L-BFGS doesn't use constraints or call do_em_step
Feature #1104: Implement dihedral restraints
Feature #1120: Make build work with multi-cofiguration generators
Feature #1137: Proposal for integrator framework (do_md) in future GROMACS
Feature #1142: Synchronizing the differences between point estimation and histogram estimation for free energies
Feature #1162: Implement gb_saltconc
Feature #1165: Multi-SIMD binaries
Feature #1167: trjconv -center would be more intuitive if it centered the center of mass, not the midpoint between minimum and maximum values
Feature #1168: g_density does not do what users think it does, given PBC over z and constant pressure simulation
Feature #1182: improve trajectory writing to support parallel I/O
Feature #1221: More generic position mapping for selections
Feature #1247: fix hardcoded references to atom names in analysis tools
Feature #1335: Improved interaction of free energies with pull code to better support Hamiltonian replica exchange with umbrella sampling
Feature #1347: future of tables
Feature #1397: gmx eneconv -offset 1.998 -dt 2 is broken for large times
Feature #1437: Online help formatting improvements
Feature #1464: implement PP-PME re-balancing
Feature #1518: Enable automatic build checking for newer versions
Feature #1625: Gromacs Python API
Feature #1665: improve free energy non-bonded kernel performance
Feature #1666: new approach for Verlet-scheme kernel generation
Feature #1715: improve cycle counting GPU sharing and multi-sim
Feature #1720: Manage GROMACS JIT caching
Feature #1782: OpenCL runtime/compiler version should be reported in the log...
Feature #1877: Support reading 3d-grid data from cryo-electron microscopy tomography and X-ray crystallography
Feature #1953: use more regular polymorphism for GPU code
Feature #1966: Hydrogen mass repartiniong
Feature #1972: external potential modules for refinement against experimental data
Feature #1994: explore using JIT for CUDA
Feature #2005: Full Correlation Analysis (FCA) as Trajectory Analysis Module
Feature #2034: Unit tests for bonded forces
Feature #2054: PME on GPU
Feature #2068: Access to low level classes
Feature #2070: Physical validation testing
Feature #2097: Move output of dhdl file entirely to edr, rather than having a separate text dhdl file
Feature #2132: Intermediate code for xvg handling
Feature #2137: Preliminary refactoring of constraints and update machinery.
Feature #2186: Potential change for logical improvements: move control of constraints purely to the .mdp
Feature #2229: Full Object Oriented Modularization of GROMACS MDRUN Codebase
Feature #2282: Density map toolset
Feature #2310: Let mdrun dump coordinates with non-finite energy
Feature #2354: develop configuration file support for control of task layout
Feature #2426: Trajectory analysis tool for functional mode analysis by partial least squares fitting (PLS-FMA)
Feature #2491: Allow constant bias AWH simulations
Feature #2545: Should grompp fix periodicity of input files?
Feature #2547: Add option of averaging and obtaining error bars for AWH PMFs
Feature #2574: iForceSchedule Abstraction
Feature #2579: Add dimensionality option to gmx trjconv -center
Feature #2581: User interface for hybrid Monte Carlo
Feature #2594: Multi-level GMX API
Feature #2601: Free energy calculations, soft-core potential
Feature #2622: Reduce severity of Berendsen warning
Feature #2715: Avoid requesting the user to recompile gromacs for Intel OpenCL support
Feature #2791: Implement a module for lambda-dynamics simulations (lambda_site module)
Feature #2840: Test that functionality does not compile that is not supposed to.
Feature #2866: Alternative non-bonded potentials
Feature #3069: Iterator over span and indices into this span (zip-style iterator)
Feature #3172: QM/MM Interface with CP2K
Feature #3285: Run simulations from the same tpr file with different random seeds
Task #652: Change selection method implementation to use C++
Task #665: Port existing trajectory analysis tools to use the new framework
Task #701: Add symbol visibility macros
Task #765: Improving serialization of data structures prior to communication
Task #909: Reimplement displacement calculation module
Task #986: Handling C++ out-of-memory errors
Task #988: Definition of "public API"
Task #996: C++ MPI Framework
Task #1170: mdlib reorganization
Task #1211: improve use of preprocessor macros in CUDA kernels
Task #1411: Future of thread_mpi
Task #1729: Resolve whether and how to resolve "state" variables stored in .tpr
Task #1758: Verlet scheme reorganization / modularization
Task #1768: decide future of command-line options vs env vars
Task #1781: re-design benchmarking functionality
Task #1785: no pV term written to energy file when pressure coupling is anisotropic
Task #1793: cleanup of integration loop
Task #1826: investigate non-optimal results with CPU-GPU balancing on AMD
Task #1845: consider replacing FindOpenCL with the version provided by CMake
Task #1852: Remove group scheme
Task #1876: Reorganize vector input passed to core MD routines
Task #1879: make the GROMACS OpenCL kernel work on Gallium
Task #1936: treat default-able mdp fields as strings
Task #1937: stop supporting changing CUDA host compiler
Task #1971: Removing buggy features vs. keeping workflows
Task #2017: Modularize simulation option storage and reading from mdp files
Task #2035: A common trajectory analysis data exchange format
Task #2092: Tests running on GPU, and hardware assignment
Task #2168: Design for multiple comparisons against same test reference data
Task #2175: improve clang static analyzer docs further
Task #2216: GROMACS SIMD acceleration: generation 3
Task #2304: Document and propose tracking mdrun heuristics
Task #2341: assess the state of building and using GROMACS on Windows
Task #2351: Avoid the SIMD module depending on non-trivial parts of Gromacs
Task #2367: construct pbc_simd less often
Task #2368: update implementation of gmx msd
Task #2371: mtop searching needs reconsideration
Task #2379: check leftover FIXMEs in r2018
Task #2383: Add JSON interface to write and read files
Task #2402: PME kernels general performance improvements
Task #2423: modernize constraints code
Task #2442: Port gmx saxs and gmx sans to c++
Task #2461: Expose more info from t_atom to trajectory analysis framework
Task #2490: evaluate two-step communicators
Task #2492: implement force calculation via ForceProviders containing collections of IForceProvider
Task #2498: OpenCL memory pinning/mapping
Task #2501: Documentation section on log file contents
Task #2514: PME OpenCL reductions with intrinsics
Task #2518: redesign task-assignment code for OpenCL
Task #2522: OpenCL context duplication
Task #2524: struct alignment/packing for OpenCL host & device code
Task #2527: Rename GpuEventSynchronizer to something more fitting (after mergin PME OpenCL)
Task #2528: PME GPU tuning
Task #2530: consider using CUDA Driver API
Task #2537: Simplify PME solve reduction
Task #2546: Add more assertions to AWH code
Task #2566: Refactor pdb2gmx into c++ framework
Task #2590: Essential Dynamics as module providing forces
Task #2595: Reusable Utilities for Schedules
Task #2603: Add ability to properly check coordinate files during testing
Task #2621: Fine-Grained API to Describe Force Calculation and Neighbourhood Search
Task #2632: make sure cmake defines proper hwloc versionc with cross-compilation enabled
Task #2644: Replace compute_globals
Task #2650: revise OpenCL stack recommendations
Task #2658: Secondary structure assignment via DSSP as native gromacs code
Task #2660: rework OpenCL nbnxn kernel constants
Task #2671: replace constants like M_PI
Task #2672: check & document execution width requirements in OpenCL
Task #2674: Improve domain decomposition for bilayer systems
Task #2696: ensure PME queue is flushed
Task #2697: improve FFT library flavor/version reporting
Task #2735: Allow gmx_genrestr to write correct position restraints for molecules after the first molecule
Task #2758: Modernize genconf
Task #2771: Size independent Hessian for normal mode analysis
Task #2822: Make nbnxn a module
Task #2861: import an implementation of c++17 std::optional
Task #2889: update grompp warnings for brevity, usefulness and actionability
Task #2947: make an end to end test for membed
Task #2988: clean up and refactor code to modern standards
Task #2992: Split hw_opt in const user options and dynamic settings
Task #3106: Implement multiple pulses with GPU communication
Task #3267: Document tools
Task #3306: Document gmx dos tool more clearly
Task #3331: Run physical validation tests in Gitlab