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# Project Tracker Status Priority Subject Assignee Updated Target version
2283 GROMACS Feature New Normal Force distribution analysis Bernd Doser 10/27/2017 11:44 AM
3378 GROMACS Feature New Normal genion usage without stdin (facilitates use in gmx python api) 02/13/2020 12:04 PM
3332 GROMACS Feature New Normal gmx helixorient doesn't have a -tu option to change time unit 01/22/2020 11:57 AM
2288 GROMACS Feature Accepted Low gmx msd doesn't optimally handle missing input trajectory frames 11/10/2017 11:03 AM
1602 GROMACS Feature New Low gmx order S per slice along all 3 axes 09/22/2014 07:25 AM
2289 GROMACS Feature New Normal gmx spatial add ability to perform over multiple reference structures 11/08/2017 12:31 AM
3362 GROMACS Feature New Normal gmx traj: add an option to plot each component in a separate file 01/29/2020 06:18 PM
3134 GROMACS Feature Feedback wanted Normal gmxapi Python exception names may need improvement Eric Irrgang 10/13/2019 01:50 PM
2915 GROMACS Feature In Progress High GPU direct communications 02/14/2020 12:48 PM
2254 GROMACS Feature New Normal GPU extensions for Google Tests 09/19/2017 05:01 PM
1688 GROMACS Feature New Low g_cluster "middle" is not exactly the same as the definition in the cited paper 04/01/2015 05:53 AM
1498 GROMACS Feature New Low g_dipoles does not work properly with ionic systems David van der Spoel 07/11/2016 08:11 PM
843 GROMACS Feature New Low g_helixorient could benefit from more documentation Erik Lindahl 05/23/2014 02:02 PM
2226 GROMACS Feature New Normal Harmonise commands for exit in make_ndx and distance 08/04/2017 12:24 PM
2961 GROMACS Feature New Normal How should Python package find GROMACS resources under various circumstances? 12/09/2019 10:47 AM
1654 GROMACS Feature New Normal How to carry out movement between chemical end states in a multiple end state framework? Michael Shirts 07/11/2016 08:05 PM
2111 GROMACS Feature In Progress Normal Implement Gaussian screening of electrostatics 02/23/2019 12:33 PM
2126 GROMACS Feature New Normal implement native CUDA support in CMake 10/29/2019 09:03 PM
1900 GROMACS Feature New Normal Implement some new errors in grompp 06/22/2016 05:20 PM
1083 GROMACS Feature In Progress Normal Improve collective error/warning/note handling in mdrun 07/11/2016 08:21 PM
3138 GROMACS Feature New Normal Improve ensemble support in Context specification. 10/15/2019 03:56 PM
2585 GROMACS Feature Resolved Normal Infrastructure supporting external API 12/11/2019 12:39 PM
1562 GROMACS Feature New Normal introducing a Monte Carlo framework (first application: MC barostat) Michael Shirts 07/11/2016 08:08 PM
2248 GROMACS Feature New Normal Label all SIMD functions as pure/nodiscard 02/04/2019 04:49 AM
2930 GROMACS Feature New Normal Limited range for reference group detection in cylinder pulling 04/26/2019 05:17 PM
2761 GROMACS Feature New Low lincs-order 4 is too conservative for some force fields 11/16/2018 09:55 AM
2451 GROMACS Feature Resolved Normal Linear virtual sites with fixed distance David van der Spoel 09/16/2019 01:15 PM
2975 GROMACS Feature New Normal LJ PME calculations on GPUs 06/12/2019 01:17 PM
1867 GROMACS Feature New Normal make coupling implementations reversible 12/02/2015 07:43 AM
2556 GROMACS Feature New Normal make default selections suitable for DNA and RNA Mark Abraham 06/20/2018 01:48 PM
3135 GROMACS Feature New Normal Make GPU traits ino opaque types 10/14/2019 10:24 AM
2188 TNG trajectory library Feature Resolved High Masses missing from TNG specification Magnus Lundborg 06/13/2017 05:08 PM
2755 GROMACS Feature New Low md5 sums and sha256, sha512 hashes Benson Muite 02/19/2019 11:00 PM
2643 GROMACS Feature New Low mdp options and/or docs for anisotropic aspects of implementations 09/12/2018 02:23 PM
2910 GROMACS Feature New Normal Mixed scaling for 1-4 interactions 04/10/2019 10:13 PM
3020 GROMACS Feature New Low modernize DeviceBuffer and GPU memory management 08/13/2019 06:01 PM
2984 GROMACS Feature New Normal More Extensive Selections Examples Dallas Warren 06/18/2019 11:50 PM
2139 GROMACS Feature New Normal More precise/explicit documentation conventions 01/07/2018 11:54 PM
2118 GROMACS Feature New Low More verbose comments requested in header of gmx distance -oxyz 02/08/2017 05:46 AM
1328 GROMACS Feature Accepted Normal Names for selection positions 07/11/2016 08:15 PM
3355 GROMACS Feature Accepted Normal New PME parallel (GPU) scheme Jonathan Vincent 02/12/2020 11:58 AM
3439 GROMACS Feature New Normal Optimize successive simulation segments 03/11/2020 01:42 PM
2860 GROMACS Feature New Normal Option for outputting min/max coordinates in gmx traj 02/08/2019 12:35 AM
3045 GROMACS Feature New Low Option to remove v-sites in trjconv? 07/19/2019 04:42 PM
2739 GROMACS Feature New Normal Parallel continuous tempering and enhanced sampling feature 11/13/2018 11:36 PM
950 GROMACS Feature New Normal Path/directory/filename handling in Gromacs 07/11/2016 08:24 PM
731 GROMACS Feature New Normal pdb2gmx should warn about missing residues when bonds are too long 06/22/2014 10:55 AM
3242 GROMACS Feature New Normal Please do not remove the -nsteps flag 03/01/2020 01:59 PM
2891 GROMACS Feature In Progress Normal PME/PP GPU communications 02/14/2020 12:40 PM
1500 GROMACS Feature New Normal Post-5.0 feature clean-up plan Mark Abraham 08/26/2019 03:47 PM
2977 GROMACS Feature New Normal print DD load balancing improvement 06/13/2019 10:56 AM
1105 Benchmark suite Feature New Normal produce a benchmark suite 09/13/2016 10:31 PM
1635 GROMACS Feature New Normal Proper Unicode support 06/18/2015 08:34 PM
2587 GROMACS Feature In Progress Normal Provide Context (e.g. to runner code) to manage client and runtime environment 10/15/2018 03:34 PM
1106 Benchmark suite Feature New Normal publish benchmark numbers 06/19/2014 12:08 PM
2018 GROMACS Feature New Normal Pulling along a line between given points 07/27/2016 09:59 AM
3149 GROMACS Feature New Normal Python user interface for obtaining simulation artifacts as files. Eric Irrgang 10/15/2019 06:21 PM
2090 GROMACS Feature New Normal redirecting stdout or stderr for testing Mark Abraham 12/15/2016 03:15 AM
2180 Support Platforms Feature Fix uploaded Low releng matrices would work better with a hint for execution 05/19/2017 01:02 AM
1854 GROMACS Feature New Normal Remove all cyclic dependencies 05/25/2017 08:34 AM
2056 GROMACS Feature New Low rename "gmx select" 10/03/2016 08:24 PM
1842 GROMACS Feature New Normal Replace XML with JSON 01/18/2018 05:12 PM
1377 GROMACS Feature Feedback wanted Low Replica exchange if replicas not in ascendent T David van der Spoel 06/23/2016 03:48 PM
1974 GROMACS Feature New Normal Report atom numbers and types in the error message about missed parameters 05/30/2016 09:24 AM
2220 GROMACS Feature New Normal report relevant env var behaviour to console 07/31/2017 09:40 PM
1026 GROMACS Feature New Low request for gen_vel to work with multiple temperature coupling groups at different temperatures 11/17/2016 04:39 PM
3030 GROMACS Feature New Normal RST style guidelines 07/09/2019 03:38 PM
2956 GROMACS Feature New Normal SAXS resolution 05/17/2019 09:58 AM
2993 GROMACS Feature New Normal Scalar and structured type expression and definitions for API Eric Irrgang 10/17/2019 09:55 AM
2846 GROMACS Feature New Low Set rpath in FindLibStdCpp.cmake 02/02/2019 08:09 AM
2099 Support Platforms Feature New High sharing accounts/credentials 12/06/2017 08:11 PM
2207 GROMACS Feature New Normal solvent excluded volume of large molecule with periodic boundary condition 06/16/2017 10:37 AM
3177 GROMACS Feature New Normal Spack package management support 11/06/2019 06:37 PM
2239 GROMACS Feature New Normal split libgromacs into base and full 01/07/2019 01:47 AM
3298 GROMACS Feature New Normal start early PP work for first dimension of halo exchange 03/01/2020 01:36 PM
3126 GROMACS Feature New Normal State propagator GPU data manager 10/09/2019 02:42 PM
1332 GROMACS Feature In Progress Normal Supporting multiple end states instead of just A and B Michael Shirts 06/05/2018 03:58 PM
2931 GROMACS Feature New Normal Tables in Verlet kernels 04/29/2019 12:01 PM
1028 GROMACS Feature New Normal Tool to calculate fraction of native contacts during simulation 11/01/2012 10:27 PM
1601 Support Platforms Feature New Normal use Git for Jenkins Config 05/24/2015 10:59 AM
2101 GROMACS Feature New Low warninp could print the offending line, as well as its number 01/20/2017 03:06 PM
694 Support Platforms Feature Feedback wanted Normal Write instructions/policy for issue handling Rossen Apostolov 05/31/2017 05:41 PM
1864 GROMACS Feature New Normal write tng files with energies Magnus Lundborg 07/11/2016 08:00 PM
2194 GROMACS Feature Accepted Low xvg output requested as an output option in place of xpm files 05/31/2017 04:26 PM
3300 GROMACS Task New Normal Abandon docs/OpenCLTODOList.txt? 01/15/2020 02:46 PM
2905 GROMACS Task New Normal Add a Jenkins configuration with std library assert 08/24/2019 05:22 PM
2456 GROMACS Task New Normal Add a pull module external potential tests 03/15/2018 03:02 PM
2185 GROMACS Task New Normal add docs on MPI + CUDA w/wo MPS 05/24/2017 05:17 PM
1523 GROMACS Task New Normal add missing code-paths to CUDA emulation kernel 07/11/2016 08:09 PM
1373 GROMACS Task New Low Add missing nbnxn tests Mark Abraham 06/09/2014 08:36 PM
3268 GROMACS Task New Normal add more Intel driver recommendations 12/26/2019 04:39 PM
2682 GROMACS Task New Normal Add MSAN configuration 10/09/2018 06:28 PM
920 GROMACS Task In Progress Normal Add test framework for trajectory analysis modules Teemu Murtola 07/11/2016 08:27 PM
3123 GROMACS Task New Normal address sanitizer coverage of parallelization code-paths 10/05/2019 12:32 AM
2855 GROMACS Task New Normal Allow compiling GROMACS without C compiler 01/10/2020 12:06 PM
3078 GROMACS Task New Normal Allow MD modules to register energy output fields themselves 09/06/2019 11:36 AM
2787 GROMACS Task New Normal allow passing flags to allocateDeviceBuffer 12/03/2018 01:54 PM
2045 GROMACS Task New Normal API design and language bindings Peter Kasson 01/29/2020 03:59 PM
3446 GROMACS Task New Normal apply maintainability updates across all GPU kernels Jonathan Vincent 03/19/2020 03:31 PM
2850 GROMACS Task In Progress Normal assess Raptor Talos for testing Szilárd Páll 02/12/2019 01:14 PM
2412 GROMACS Task New Normal attempt to do better FFTW planning 03/15/2018 05:01 PM
2221 GROMACS Task New Normal Avoid preprocessor for SIMD functions 02/21/2018 01:43 PM
2478 GROMACS Task New Low avoid use of getenv in static initialization 04/13/2018 11:57 AM
2983 GROMACS Task New Normal better suited data-types for bonded GPU kernels 07/11/2019 04:32 PM
1010 GROMACS Task In Progress Normal Better support for multiple AnalysisData datasets Teemu Murtola 07/11/2016 08:23 PM
2818 GROMACS Task In Progress Normal bonded GPU kernel fusion Magnus Lundborg 07/03/2019 09:01 PM
2864 GROMACS Task New Normal Building incompatibilties Benson Muite 02/19/2019 02:00 PM
2919 GROMACS Task New Normal C++ style guidelines for namespace use 04/15/2019 01:21 PM
948 GROMACS Task New Normal C++ thread synchronization primitives Sander Pronk 07/11/2016 08:24 PM
1017 GROMACS Task New Normal C++ Vector/Matrix classes 07/11/2016 08:23 PM
2048 GROMACS Task New Normal C++11: CUDA dependency on general headers 09/07/2016 10:30 PM
2859 GROMACS Task Resolved Normal Change ArrayRef iterator type from pointer to std::iterator 06/26/2020 06:15 PM
2375 GROMACS Task New Normal Clarify execution phases for MD simulation 04/30/2019 12:59 PM
2857 GROMACS Task New Normal Clarify recommended function specifies (constexpr, noexcept, pure) 02/04/2019 04:48 AM
2796 GROMACS Task New Low clarify what mdrun -cpt means 01/03/2019 02:09 PM
1140 GROMACS Task New Normal Class design for passing options and data 07/11/2016 08:19 PM
1963 GROMACS Task New Low collect examples of systems where users tried to do something that performed badly Mark Abraham 08/09/2016 07:30 AM
2158 GROMACS Task New Normal consider adding post-submit test that runs PME with 2xNN kernels 04/19/2017 08:04 PM
2462 GROMACS Task New Normal consider adding STL misuse tests 03/23/2018 01:23 AM
2535 GROMACS Task New Normal consider compiling opencl fft kernels once 05/31/2018 01:33 PM
1947 GROMACS Task New Normal Consider fixing corner case in TinyXML2 Mark Abraham 04/19/2016 01:40 AM
2909 GROMACS Task New Normal consider implementing mechanisms to ensure pair lists are not used past their max lifetime 04/03/2019 05:14 PM
3365 GROMACS Task New Low consider making GPU bonded work independent from nonbonded 03/01/2020 01:11 PM
2531 GROMACS Task New Low Consider optimizing tabulated data access on GPU 07/30/2018 12:31 PM
3194 GROMACS Task New Normal consider passing GPU dependency list to both dependency producers and consumers 11/01/2019 07:10 PM
3002 GROMACS Task New Normal consider splitting bonded work into local/nonlocal 06/25/2019 04:06 PM
837 Support Platforms Task Resolved Low Consider subproject organization of the Gromacs project 07/14/2014 12:07 PM
3181 GROMACS Task New Normal consolidate task assignment and workload data initialization 10/28/2019 02:53 PM
3201 GROMACS Task In Progress Normal Convert mdp parameters to key value tree 11/06/2019 06:06 PM
1855 GROMACS Task New Normal Convert preprocessor use so that symbols are always defined 06/28/2016 02:17 PM
2933 GROMACS Task New Normal Convert walls to a ForceProvider 04/25/2019 02:43 PM
3445 GROMACS Task New Normal create heuristic for c_skipNeutralAtoms Jonathan Vincent 03/17/2020 12:12 PM
2182 GROMACS Task New Low de-duplicate code in densorder and hydorder 05/16/2017 11:29 AM
2445 GROMACS Task New Normal Decide if/how to check for incompatible user input to mdrun for bonds and vsites 03/13/2018 02:02 PM
3287 GROMACS Task New Normal Deprecate make_ndx, use select instead 01/23/2020 01:16 PM
1323 GROMACS Task New Normal determine future of existing tools for David van der Spoel 12/04/2018 11:53 AM
3289 GROMACS Task New Normal Distinguish identifying and non-identifying inputs to API operations. Eric Irrgang 01/10/2020 11:30 AM
3353 GROMACS Task New Normal Document gmx densmap output 01/23/2020 12:52 PM
2532 GROMACS Task New Normal enable queue priorities in OpenCL 05/29/2018 02:29 PM
2089 GROMACS Task New Normal Encourage code review 01/10/2017 12:03 AM
3366 GROMACS Task New Normal Enforce compability of MdModules 02/28/2020 11:20 AM
2882 GROMACS Task New Normal evaluate different storage layouts for GPU coordinates/changes/forces Szilárd Páll 03/07/2019 06:21 PM
1828 GROMACS Task New Normal Exception handling in mdrun 10/07/2015 11:36 AM
1246 GROMACS Task New Normal expanded ensemble .tpr cannot be rerun Michael Shirts 06/19/2015 01:56 PM
2496 GROMACS Task New Low find system xdr properly 05/02/2018 02:19 PM
1862 GROMACS Task New Normal Fully replace t_topology by gmx_mtop_t 02/13/2019 04:53 PM
3370 GROMACS Task New High Further improvements to GPU Buffer Ops and Comms 03/04/2020 01:38 PM
1829 GROMACS Task New Normal Future of thread level parallelism 11/18/2016 05:29 PM
2133 GROMACS Task New Low gmx traj needs reform 03/07/2017 02:02 PM
2166 GROMACS Task Accepted Normal gmx trjconv functionality should check for mismatch between the tpr and the trajectory 05/05/2017 04:32 PM
3139 GROMACS Task New Normal gmxapi Futures should be subscribable Eric Irrgang 10/15/2019 03:56 PM
3132 GROMACS Task New Normal gmxapi testing support tools 10/31/2019 03:35 PM
2764 GROMACS Task New Normal gmxapi version updates for post release-2019 Eric Irrgang 11/21/2018 12:53 PM
2240 GROMACS Task Accepted Low GPU emulation mode support for PME missing 09/16/2017 10:02 PM
2238 GROMACS Task In Progress Normal GPU emulation mode support for rolling pruning missing Berk Hess 12/21/2017 03:21 PM
2464 GROMACS Task New Normal GPU performance goals overview 03/26/2018 10:42 AM
2435 GROMACS Task New Normal identify and note about/tune task offload in GPU-bound runs 03/02/2018 04:08 PM
2521 GROMACS Task New Normal Implement alternating PME/NB wait for OpenCL 10/15/2018 12:39 PM
1815 Support Platforms Task In Progress Normal implement and execute plan for new releng machinery 10/15/2016 05:37 PM
2469 GROMACS Task New Normal implement GPU timer reduction for reporting 03/27/2018 05:08 PM
3003 GROMACS Task New Normal implement heuristic fallback to CPU when there is too little work for GPU offload 06/25/2019 04:10 PM
2009 GROMACS Task New Normal improve command-line reporting of useful things 07/26/2016 12:54 PM
3216 GROMACS Task New Normal improve CPU force reductions Szilárd Páll 12/04/2019 09:24 PM
838 GROMACS Task New Normal Improve generic error reporting routines 07/11/2016 08:29 PM
1515 GROMACS Task New Normal improve g_bar output Szilárd Páll 07/11/2016 08:10 PM
1505 GROMACS Task New Normal improve handling of logging Mark Abraham 01/02/2019 06:06 PM
2863 GROMACS Task New Normal improve PBC handling 03/11/2019 04:28 PM
2519 GROMACS Task New High Improve/remove PME OpenCL kernel barriers 02/15/2019 06:34 PM
2792 GROMACS Task New High Improvement of PME gather and spread CUDA kernels 03/18/2020 03:57 PM
3016 GROMACS Task New Normal intermittent failure of essentialdynamics test 07/18/2019 05:23 PM
3360 GROMACS Task New Normal investigate the future of DD dynamic load balancing with GPU offload 01/29/2020 11:23 AM
1309 Support Platforms Task New Normal Jenkins verification improvements 06/01/2017 02:34 PM
1214 GROMACS Task New Normal Keep track of important changes for Changelog Mark Abraham 06/26/2013 11:24 AM
1907 GROMACS Task Accepted Low keeping compile- and run-time CPU/arch detection consistent 08/01/2016 10:09 PM
629 Support Platforms Task In Progress Normal List of users needs cleanup Rossen Apostolov 02/21/2018 02:07 PM
2071 GROMACS Task In Progress High Low accuracy default settings yield incorrect liquid densities Berk Hess 01/05/2018 03:32 PM
869 GROMACS Task In Progress Normal Make analysis data histogramming and multipoint data easier to use in parallel Teemu Murtola 07/11/2016 08:28 PM
3357 GROMACS Task New Normal Make sure "colvars" interoperates stably and smoothly with gromacs 03/04/2020 11:25 AM
677 GROMACS Task New Normal Make sure manual uses consistent style throughout 06/19/2014 11:49 AM
2835 GROMACS Task New Normal Matrix class constraint to upper or lower triangle 02/07/2019 02:44 PM
2376 GROMACS Task New Normal max_mpi_ranks has wrong name 02/10/2018 11:03 AM
2616 GROMACS Task New Normal Model for MD state 09/14/2018 05:12 PM
3255 GROMACS Task New Normal Move benchmarking options from mdrun to a dedicated tool 12/19/2019 01:21 PM
2178 GROMACS Task New Normal Move checks for specific warnings to source repo 05/12/2017 03:57 PM
3005 GROMACS Task New Normal Move logging in gmx preprocess to MDLogger 06/26/2019 10:01 AM
3004 GROMACS Task New Normal Move trajectory analysis logging to MDLogger 06/26/2019 09:59 AM
1745 GROMACS Task New Normal Moving to C++11 after Gromacs-5.1 06/01/2016 03:01 PM
2084 GROMACS Task New Low MPI and stderr/log output 11/28/2016 06:37 PM
2898 GROMACS Task New Low Naming common variables 03/26/2019 11:46 PM
1530 GROMACS Task New Low Offer binary downloads 06/29/2014 02:58 PM
1973 GROMACS Task New Normal OpenCL implementation wish list 05/27/2016 03:42 PM
2538 GROMACS Task New Normal organize more of the PME GPU code along task-specific lines Mark Abraham 05/31/2018 05:41 PM
2463 GROMACS Task New Low PME GPU decomposition 03/26/2018 10:42 AM
3077 GROMACS Task Feedback wanted Normal PME/PP GPU Comms unique pointer deletion causes seg fault when CUDA calls exist in destructor 11/01/2019 06:56 PM
3174 GROMACS Task Feedback wanted Low Proposed gmxapi syntax update: "input" and "output" key word arguments -> "inputs" and "outputs" Eric Irrgang 10/23/2019 06:34 PM
3279 GROMACS Task New Low Provide more advice for building client software 03/02/2020 11:54 AM
1786 GROMACS Task New Normal Python style standards in developer docs Peter Kasson 12/26/2019 03:15 PM
2003 GROMACS Task New Normal reconsider various simd flags 07/07/2016 11:23 PM
2452 GROMACS Task In Progress Normal Reduce data dependencies in mdrun algorithms Berk Hess 03/14/2018 08:47 PM
1509 GROMACS Task New Low Reduce the distance dependence of shifted potentials for free energies if possible Michael Shirts 07/11/2016 08:10 PM
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