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# Project Tracker Status Priority Subject Assignee Updated Target version
1105 Benchmark suite Feature New Normal produce a benchmark suite 09/13/2016 10:31 PM
1106 Benchmark suite Feature New Normal publish benchmark numbers 06/19/2014 12:08 PM
2756 GROMACS Task In Progress Normal gmxapi integration testing 01/16/2020 05:12 PM GROMACS - 2021-refactoring
2896 GROMACS Feature Feedback wanted Normal Python packaging 01/16/2020 07:11 PM GROMACS - 2021-refactoring
2967 GROMACS Feature New Normal GPU reallocateDeviceBuffer improvements 01/23/2020 12:15 PM GROMACS - 2021-refactoring
3033 GROMACS Task In Progress Normal Clean up and modernize googletest bundling and usage 01/16/2020 04:50 PM GROMACS - 2021-refactoring
3290 GROMACS Task Resolved Normal Require CMake >= 3.12 04/14/2020 02:45 PM GROMACS - 2021-refactoring
3307 GROMACS Feature New Normal General interface for communication between simulation ranks 01/22/2020 03:22 PM GROMACS - 2021-refactoring
3311 GROMACS Feature In Progress Normal GPU infrastructure development 03/20/2020 09:54 AM GROMACS - 2021-refactoring
3324 GROMACS Task New Normal Rework CMake handling of GPU code 01/22/2020 09:52 AM GROMACS - 2021-refactoring
3325 GROMACS Task New Normal Allow complete re-initialization of a simulation 01/29/2020 05:13 PM GROMACS - 2021-refactoring
3326 GROMACS Task New Normal Allow changing task assignment 01/22/2020 09:44 AM GROMACS - 2021-refactoring
3327 GROMACS Task New Normal Refactor workload flags 01/22/2020 09:45 AM GROMACS - 2021-refactoring
3328 GROMACS Feature New Normal Testing framework for task assignment 01/22/2020 09:48 AM GROMACS - 2021-refactoring
3329 GROMACS Task New Normal Extend energy comparison testing framework 01/22/2020 09:51 AM GROMACS - 2021-refactoring
3330 GROMACS Task New Normal Compile list of codepaths for testing task assignment 01/22/2020 10:03 AM GROMACS - 2021-refactoring
3374 GROMACS Feature New Normal SimulationInput abstraction 03/03/2020 05:32 PM GROMACS - 2021-refactoring
2958 GROMACS Bug New Normal Compiling master (to become 2020) using CUDA 9.0 03/02/2020 03:57 PM GROMACS - 2020.2
2974 GROMACS Bug New Normal position-restraints regressiontest fails on intel GPU with OpenCL 02/25/2020 03:52 PM GROMACS - 2020.2
3021 GROMACS Feature Feedback wanted Normal Completion of docs for GPU developments 03/02/2020 03:58 PM GROMACS - 2020.2
3125 GROMACS Bug Resolved Normal OpenCL on Volta and Turing borken 02/27/2020 11:01 AM GROMACS - 2020.2
2481 GROMACS Task New Low Update gmx report-methods to write more method information 12/02/2019 01:22 PM GROMACS - 2021-infrastructure-stable
2698 GROMACS Task In Progress Normal gmxapi documentation integration 01/29/2020 03:59 PM GROMACS - 2021-infrastructure-stable
2699 GROMACS Task New Normal Test POWER9 12/04/2019 03:29 PM GROMACS - 2021-infrastructure-stable
2706 GROMACS Task Accepted Normal Rework classic QM/MM interface 12/02/2019 01:45 PM GROMACS - 2021-infrastructure-stable
2795 GROMACS Task New Normal Incorporate regressiontests into core gromacs 12/02/2019 01:44 PM GROMACS - 2021-infrastructure-stable
2994 GROMACS Feature New Normal Data flow topology in gmxapi 2020 12/11/2019 11:33 AM GROMACS - 2021-infrastructure-stable
2998 GROMACS Task Resolved Normal Update Python detection 04/23/2020 04:45 PM GROMACS - 2021-infrastructure-stable
2999 GROMACS Task New Normal Move all logging in core library and tools to use MDLogger 09/06/2019 02:36 PM GROMACS - 2021-infrastructure-stable
3010 GROMACS Task In Progress Normal upgrade OpenCL stack on bs-gpu01 12/20/2019 08:25 AM GROMACS - 2021-infrastructure-stable
3013 GROMACS Task New Normal Extend logging levels in MDLogger 09/06/2019 02:34 PM GROMACS - 2021-infrastructure-stable
3014 GROMACS Task In Progress Normal gmxapi example Python scripts 01/03/2020 11:00 AM GROMACS - 2021-infrastructure-stable
3015 GROMACS Task New Normal Create central log handle for calls to gmx_fatal 09/06/2019 02:34 PM GROMACS - 2021-infrastructure-stable
3032 GROMACS Feature Feedback wanted Normal Clean up dev-manual structure 12/11/2019 11:27 AM GROMACS - 2021-infrastructure-stable
3093 GROMACS Task In Progress High rework GPU direct halo-exchange related force reduction complexities 02/14/2020 11:35 AM GROMACS - 2021-infrastructure-stable
3152 GROMACS Feature New Normal Infrastructure and patterns for expressing public interfaces 01/09/2020 05:19 PM GROMACS - 2021-infrastructure-stable
3153 GROMACS Task New Low Let CMake process module directories earlier to support more modern CMake idioms. 10/17/2019 10:40 AM GROMACS - 2021-infrastructure-stable
3171 GROMACS Task New Normal schedule CPU H2D force contribution in separate stream 12/20/2019 08:33 AM GROMACS - 2021-infrastructure-stable
3183 GROMACS Task Accepted Normal enable bonded interactions on GPU 12/20/2019 08:32 AM GROMACS - 2021-infrastructure-stable
3197 GROMACS Bug New Normal Rework usage of gitattributes and filter in source code formatting scripts 11/04/2019 12:50 PM GROMACS - 2021-infrastructure-stable
3220 GROMACS Task New Normal change rolling pruning scheduling with GPU update 02/25/2020 03:41 PM GROMACS - 2021-infrastructure-stable
3229 GROMACS Task New Normal Move checkpointing to the beginning of the MD step 01/16/2020 04:31 PM GROMACS - 2021-infrastructure-stable
3271 GROMACS Task Resolved Normal Adopt PEP-518 for Python package build system configuration. 04/09/2020 10:15 PM GROMACS - 2021-infrastructure-stable
3273 GROMACS Bug New Normal gmxapi setup.py complains too much 12/27/2019 06:42 PM GROMACS - 2021-infrastructure-stable
3274 GROMACS Bug New Normal Remove ARM NEON SIMD 12/28/2019 07:53 AM GROMACS - 2021-infrastructure-stable
3288 GROMACS Feature New Normal Use build system infrastructure instead of custom scripts to manage API levels. 02/26/2020 04:16 PM GROMACS - 2021-infrastructure-stable
3297 GROMACS Task Resolved Normal Require gcc > 5 04/30/2020 11:00 AM GROMACS - 2021-infrastructure-stable
3308 GROMACS Task New Normal GPU update-constraints: Cycle counting for GPU launches 01/23/2020 11:54 AM GROMACS - 2021-infrastructure-stable
3379 GROMACS Feature New Normal C++ API for simulation input and output 02/28/2020 10:38 AM GROMACS - 2021-infrastructure-stable
3401 GROMACS Feature New Normal Policy and procedure for installed headers (public API) 02/26/2020 04:17 PM GROMACS - 2021-infrastructure-stable
3402 GROMACS Feature New Normal Clarify distinction between public API documentation and developer docs. 02/26/2020 04:16 PM GROMACS - 2021-infrastructure-stable
3411 GROMACS Bug New Normal Nightly master release build failure 03/06/2020 11:44 AM GROMACS - 2021-infrastructure-stable
1587 GROMACS Task New Normal improve the configurability of regression tests 12/20/2019 12:02 PM GROMACS - 2021
1925 GROMACS Task In Progress Normal remove concept of unilateral global communication 12/29/2019 10:35 AM GROMACS - 2021
1985 GROMACS Bug Fix uploaded Low CUDA build system refactoring awaiting review 12/20/2019 12:07 PM GROMACS - 2021
2053 GROMACS Task New Normal refine notation in GPU code 12/20/2019 01:04 PM GROMACS - 2021
2059 GROMACS Task In Progress Normal Separate different types of data in t_state 12/27/2019 04:42 PM GROMACS - 2021
2169 GROMACS Task New Normal remove 'continuation' mdp option 12/29/2019 10:31 AM GROMACS - 2021
2353 GROMACS Task New Normal improve on relative tolerance for constructing tables 12/20/2019 12:12 PM GROMACS - 2021
2390 GROMACS Bug Feedback wanted Normal GROMACS build system should check for valid nvcc flags before use 12/20/2019 12:13 PM GROMACS - 2021
2475 GROMACS Task New Normal make OpenCL 1st class-citizen in the build system 12/20/2019 12:14 PM GROMACS - 2021
2675 GROMACS Task In Progress Normal bonded CUDA offload task 02/12/2020 05:54 PM GROMACS - 2021
2686 GROMACS Task New Normal add tests for gpu bonded interactions 12/27/2019 04:40 PM GROMACS - 2021
2695 GROMACS Task New Low bonded GPU module timing 12/27/2019 04:40 PM GROMACS - 2021
2710 GROMACS Feature New Normal Separate dvdl for each molecule (of couple-moltype) when running FEP 12/27/2019 04:41 PM GROMACS - 2021
2770 GROMACS Task New Normal change branch maintenance policy 01/16/2020 05:09 PM GROMACS - 2021
2773 GROMACS Task New Normal improve GPU error handling and make such handling uniform across modules 12/20/2019 01:09 PM GROMACS - 2021
2806 GROMACS Feature New Normal SIMD algorithms for ARM SVE // nobnonded cluster and otheres 12/27/2019 03:59 PM GROMACS - 2021
2839 GROMACS Task New Normal make module and file naming consistent 01/16/2020 05:11 PM GROMACS - 2021
2890 GROMACS Feature In Progress Normal GPU Halo Exchange 02/14/2020 12:41 PM GROMACS - 2021
2936 GROMACS Task New Normal introduce check that CPU-GPU transfers/assignments are made between compatible types 02/05/2020 03:57 PM GROMACS - 2021
2965 GROMACS Task In Progress Normal Performance of GPU direct communications 02/14/2020 12:38 PM GROMACS - 2021
2976 GROMACS Task New Normal Basic math for Multidimensional arrays 12/27/2019 04:37 PM GROMACS - 2021
2987 GROMACS Bug New Normal assess the bonded GPU task assignment default 12/20/2019 01:06 PM GROMACS - 2021
2997 GROMACS Task New Normal improve performance of alchemical free energy calculations 12/27/2019 04:31 PM GROMACS - 2021
3001 GROMACS Task New Normal explore simplifying virial and shift force reduction 12/27/2019 04:30 PM GROMACS - 2021
3008 GROMACS Task New Normal verify block size choice of CUDA bonded kernel 12/27/2019 04:30 PM GROMACS - 2021
3031 GROMACS Task New Normal evaluate the impact of particle order on PME 12/27/2019 04:29 PM GROMACS - 2021
3062 GROMACS Task New Normal add twin cut-off mdrun test 12/27/2019 04:22 PM GROMACS - 2021
3064 GROMACS Task New Normal add test for perturbed bonded forces 12/27/2019 04:22 PM GROMACS - 2021
3082 GROMACS Task New High move launch/synchronization points to clarify task dependencies 12/27/2019 04:21 PM GROMACS - 2021
3104 GROMACS Task New Normal implement GPU DD cycle counting 12/27/2019 04:21 PM GROMACS - 2021
3105 GROMACS Task New Normal implement GPU PME/PP comm cycle counting 12/27/2019 04:20 PM GROMACS - 2021
3119 GROMACS Task New Normal clang-tidy coverage of parallelizaton codepaths 12/27/2019 04:20 PM GROMACS - 2021
3124 GROMACS Bug New Normal significant performance loss due to DLB auto-off when PP/PME load >1 01/28/2020 02:44 PM GROMACS - 2021
3224 GROMACS Task New Normal add regression test case large enough to miscalculated GPU grid launch cases 12/20/2019 01:18 PM GROMACS - 2021
3277 GROMACS Feature New Normal Allow testing feature that is partly implemented 12/31/2019 12:44 PM GROMACS - 2021
3283 GROMACS Feature Resolved Normal Support for the string method with swarms of trajectories in GROMACS 03/01/2020 01:16 PM GROMACS - 2021
3356 GROMACS Task New Normal Expose setting of random seed to API 01/29/2020 06:16 PM GROMACS - 2021
677 GROMACS Task New Normal Make sure manual uses consistent style throughout 06/19/2014 11:49 AM
731 GROMACS Feature New Normal pdb2gmx should warn about missing residues when bonds are too long 06/22/2014 10:55 AM
838 GROMACS Task New Normal Improve generic error reporting routines 07/11/2016 08:29 PM
921 GROMACS Feature Blocked, need info Normal Default index groups and selections 07/11/2016 08:27 PM
950 GROMACS Feature New Normal Path/directory/filename handling in Gromacs 07/11/2016 08:24 PM
1017 GROMACS Task New Normal C++ Vector/Matrix classes 07/11/2016 08:23 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
1028 GROMACS Feature New Normal Tool to calculate fraction of native contacts during simulation 11/01/2012 10:27 PM
1083 GROMACS Feature In Progress Normal Improve collective error/warning/note handling in mdrun 07/11/2016 08:21 PM
1102 GROMACS Feature New Normal Detect incompletely written itp files 06/19/2014 03:23 PM
1139 GROMACS Feature New Normal Adding the possibility to arbitrarily evaluate different components in the energy/force term when the energy/force is calculated 07/11/2016 08:19 PM
1140 GROMACS Task New Normal Class design for passing options and data 07/11/2016 08:19 PM
1328 GROMACS Feature Accepted Normal Names for selection positions 07/11/2016 08:15 PM
1489 GROMACS Feature New Normal Don't solely rely on filename extension 04/30/2014 05:23 AM
1511 GROMACS Feature Accepted Normal add PDBx (ie mmcif) support 10/05/2018 07:14 PM
1523 GROMACS Task New Normal add missing code-paths to CUDA emulation kernel 07/11/2016 08:09 PM
1530 GROMACS Task New Low Offer binary downloads 06/29/2014 02:58 PM
1568 GROMACS Bug New Low inconsistent/incorrect threading checks and reporting in mdrun 05/25/2016 02:01 AM
1583 GROMACS Bug New Normal gmx msd with mol flag requires excessive memory 12/18/2017 03:34 PM
1602 GROMACS Feature New Low gmx order S per slice along all 3 axes 09/22/2014 07:25 AM
1627 GROMACS Feature In Progress Normal DPD integrator 07/11/2016 08:08 PM
1634 GROMACS Feature New Normal Boxed Molecular Dynamics 11/04/2014 04:40 PM
1635 GROMACS Feature New Normal Proper Unicode support 06/18/2015 08:34 PM
1641 GROMACS Feature New Normal Add toolchain file for Cray systems 06/06/2015 11:24 PM
1655 GROMACS Bug New Normal g_membed and box type 12/09/2014 01:33 PM
1670 GROMACS Feature New Normal create mdrun option checking mini-tool 06/23/2016 04:06 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
1745 GROMACS Task New Normal Moving to C++11 after Gromacs-5.1 06/01/2016 03:01 PM
1770 GROMACS Bug New Normal segmentation fault with free energy changes and multiple GPU's 07/14/2015 03:24 AM
1811 GROMACS Bug New Normal Extrae build issues 12/13/2017 03:43 AM
1828 GROMACS Task New Normal Exception handling in mdrun 10/07/2015 11:36 AM
1829 GROMACS Task New Normal Future of thread level parallelism 11/18/2016 05:29 PM
1842 GROMACS Feature New Normal Replace XML with JSON 01/18/2018 05:12 PM
1854 GROMACS Feature New Normal Remove all cyclic dependencies 05/25/2017 08:34 AM
1855 GROMACS Task New Normal Convert preprocessor use so that symbols are always defined 06/28/2016 02:17 PM
1862 GROMACS Task New Normal Fully replace t_topology by gmx_mtop_t 02/13/2019 04:53 PM
1867 GROMACS Feature New Normal make coupling implementations reversible 12/02/2015 07:43 AM
1885 GROMACS Feature New Normal DPD Thermostat 01/26/2016 10:17 AM
1900 GROMACS Feature New Normal Implement some new errors in grompp 06/22/2016 05:20 PM
1902 GROMACS Feature Accepted Low Add grompp check that non-excluded atoms are not too close to each other in the starting structure 02/15/2016 01:34 PM
1907 GROMACS Task Accepted Low keeping compile- and run-time CPU/arch detection consistent 08/01/2016 10:09 PM
1934 GROMACS Bug New Normal QMMM with ORCA: memory leaks, buffer overflows and much more 07/10/2016 09:26 AM
1948 GROMACS Feature New Low add warning when non-identical GPUs are used 06/12/2017 08:45 PM
1964 GROMACS Feature Accepted Normal "pull=no" should not produce warnings about "unknown" pull keywords 05/20/2016 02:37 PM
1973 GROMACS Task New Normal OpenCL implementation wish list 05/27/2016 03:42 PM
1974 GROMACS Feature New Normal Report atom numbers and types in the error message about missed parameters 05/30/2016 09:24 AM
2001 GROMACS Feature New Normal add MPI info to the mdrun log header 07/06/2016 05:21 PM
2003 GROMACS Task New Normal reconsider various simd flags 07/07/2016 11:23 PM
2009 GROMACS Task New Normal improve command-line reporting of useful things 07/26/2016 12:54 PM
2010 GROMACS Task New Normal Use size_t instead of int for indexing 07/01/2018 07:57 AM
2015 GROMACS Feature New Normal Auto recovery from dd communication error 07/28/2016 03:17 PM
2018 GROMACS Feature New Normal Pulling along a line between given points 07/27/2016 09:59 AM
2039 GROMACS Bug New Normal mdrun -pinstride defaults are too confusing 12/13/2017 04:14 AM
2048 GROMACS Task New Normal C++11: CUDA dependency on general headers 09/07/2016 10:30 PM
2055 GROMACS Task New Low Wiki registration is broken 01/20/2017 11:31 AM
2056 GROMACS Feature New Low rename "gmx select" 10/03/2016 08:24 PM
2060 GROMACS Feature New Normal Convert enum to enum class 10/17/2016 05:27 PM
2065 GROMACS Bug New Normal thread-MPI internal errors 11/08/2018 03:43 PM
2069 GROMACS Task New Low Simple thread-parallelism inside routines 11/09/2016 06:06 PM
2080 GROMACS Feature New Normal add grompp warning for suitableness for domain decomposition 11/23/2016 03:03 PM
2084 GROMACS Task New Low MPI and stderr/log output 11/28/2016 06:37 PM
2089 GROMACS Task New Normal Encourage code review 01/10/2017 12:03 AM
2094 GROMACS Bug New Normal Solvation Consistency with MARTINI forcefield water across GROMACS versions with user-specified VDW size 01/20/2017 04:56 PM
2101 GROMACS Feature New Low warninp could print the offending line, as well as its number 01/20/2017 03:06 PM
2111 GROMACS Feature In Progress Normal Implement Gaussian screening of electrostatics 02/23/2019 12:33 PM
2113 GROMACS Bug New Normal Google tests and execution order 03/05/2018 02:05 PM
2115 GROMACS Task New Normal trjconv does too many things, and combinations of them work poorly 10/02/2018 09:04 AM
2118 GROMACS Feature New Low More verbose comments requested in header of gmx distance -oxyz 02/08/2017 05:46 AM
2126 GROMACS Feature New Normal implement native CUDA support in CMake 10/29/2019 09:03 PM
2133 GROMACS Task New Low gmx traj needs reform 03/07/2017 02:02 PM
2139 GROMACS Feature New Normal More precise/explicit documentation conventions 01/07/2018 11:54 PM
2147 GROMACS Bug Feedback wanted Normal Parrinello-Rahman barostat not properly working 06/06/2017 07:53 AM
2158 GROMACS Task New Normal consider adding post-submit test that runs PME with 2xNN kernels 04/19/2017 08:04 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
2178 GROMACS Task New Normal Move checks for specific warnings to source repo 05/12/2017 03:57 PM
2182 GROMACS Task New Low de-duplicate code in densorder and hydorder 05/16/2017 11:29 AM
2185 GROMACS Task New Normal add docs on MPI + CUDA w/wo MPS 05/24/2017 05:17 PM
2194 GROMACS Feature Accepted Low xvg output requested as an output option in place of xpm files 05/31/2017 04:26 PM
2207 GROMACS Feature New Normal solvent excluded volume of large molecule with periodic boundary condition 06/16/2017 10:37 AM
2208 GROMACS Bug New Normal cuFFT linking 06/30/2017 01:58 PM
2217 GROMACS Bug New Low GPU emulation and separate PME ranks doesn't work properly 12/12/2017 11:50 AM
2218 GROMACS Feature Feedback wanted Normal A tiny feature: damping for umbrella pull 08/16/2017 07:20 PM
2220 GROMACS Feature New Normal report relevant env var behaviour to console 07/31/2017 09:40 PM
2221 GROMACS Task New Normal Avoid preprocessor for SIMD functions 02/21/2018 01:43 PM
2226 GROMACS Feature New Normal Harmonise commands for exit in make_ndx and distance 08/04/2017 12:24 PM
2231 GROMACS Bug New Normal convert-tpr aborts when saving subset of the system 01/12/2018 03:52 PM
2232 GROMACS Bug New Normal pdb2gmx can't form special bonds with terminal patched atoms 12/03/2017 01:35 PM
2233 GROMACS Bug Accepted Normal replica exchange and -append bugged? 03/05/2018 01:38 PM
2239 GROMACS Feature New Normal split libgromacs into base and full 01/07/2019 01:47 AM
2240 GROMACS Task Accepted Low GPU emulation mode support for PME missing 09/16/2017 10:02 PM
2241 GROMACS Bug New Low refdata can segfault when reading 09/07/2017 11:57 AM
2248 GROMACS Feature New Normal Label all SIMD functions as pure/nodiscard 02/04/2019 04:49 AM
2252 GROMACS Bug New Low Memory allocation failures with large page sizes during PME tuning 12/14/2017 04:27 AM
2254 GROMACS Feature Resolved Normal GPU extensions for Google Tests 10/06/2020 12:15 PM
2255 GROMACS Bug New Normal nstlist override stopped affecting the input parameter listing 12/17/2017 08:05 AM
2288 GROMACS Feature Accepted Low gmx msd doesn't optimally handle missing input trajectory frames 11/10/2017 11:03 AM
2289 GROMACS Feature New Normal gmx spatial add ability to perform over multiple reference structures 11/08/2017 12:31 AM
2294 GROMACS Task New Normal Require identical hardware on nodes on parallel runs 11/19/2017 08:54 PM
2373 GROMACS Bug New Low gmx -nice can't work 01/04/2018 11:17 AM
2375 GROMACS Task New Normal Clarify execution phases for MD simulation 04/30/2019 12:59 PM
2376 GROMACS Task New Normal max_mpi_ranks has wrong name 02/10/2018 11:03 AM
2380 GROMACS Bug New Low cycle counter issues with separate PME rank + GPUs 01/16/2018 10:21 PM
2382 GROMACS Task New Normal Simplify Doxygen guidelines 01/13/2018 12:40 AM
2393 GROMACS Bug New Normal incorrect error message with omitted command line flag before its argument 01/24/2018 11:24 PM
2412 GROMACS Task New Normal attempt to do better FFTW planning 03/15/2018 05:01 PM
2422 GROMACS Task New Normal write C kernel for tables in Verlet scheme 02/26/2018 01:38 PM
2427 GROMACS Bug New Normal gmx select gives syntax error for selection involving evaluating simple arithmetic expression 02/27/2018 05:15 PM
2428 GROMACS Feature New Normal Add way of selecting interactive arguments of pdb2gmx by string rather than an index 02/27/2018 06:28 PM
2429 GROMACS Feature New Normal Add option of periodic chain topology to pdb2gmx 03/10/2018 01:01 PM
2435 GROMACS Task New Normal identify and note about/tune task offload in GPU-bound runs 03/02/2018 04:08 PM
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
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