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# Project Tracker Status Priority Subject Assignee Updated Target version
2707 GROMACS Bug New Normal Installed OpenCL files include clh file from gpu_utils directory 10/30/2018 04:02 AM
2706 GROMACS Task Accepted Normal Rework classic QM/MM interface 12/02/2019 01:45 PM GROMACS - 2021-infrastructure-stable
2702 GROMACS Bug Accepted Normal PME gather reduction race in OpenCL (and CUDA) 03/28/2019 03:14 PM
2699 GROMACS Task New Normal Test POWER9 12/04/2019 03:29 PM GROMACS - 2021-infrastructure-stable
2698 GROMACS Task In Progress Normal gmxapi documentation integration 01/29/2020 03:59 PM GROMACS - 2021-infrastructure-stable
2697 GROMACS Task New Normal improve FFT library flavor/version reporting 12/27/2019 04:40 PM GROMACS - future
2696 GROMACS Task In Progress Normal ensure PME queue is flushed Szilárd Páll 12/31/2018 11:21 AM GROMACS - future
2693 GROMACS Bug New Normal Several memory leaks in mdrun 12/18/2018 04:22 AM GROMACS - future
2686 GROMACS Task New Normal add tests for gpu bonded interactions 12/27/2019 04:40 PM GROMACS - 2021
2682 GROMACS Task New Normal Add MSAN configuration 10/09/2018 06:28 PM
2675 GROMACS Task In Progress Normal bonded CUDA offload task 02/12/2020 05:54 PM GROMACS - 2021
2674 GROMACS Task Accepted Normal Improve domain decomposition for bilayer systems 12/07/2018 04:03 PM GROMACS - future
2672 GROMACS Task New Normal check & document execution width requirements in OpenCL 12/31/2018 11:20 AM GROMACS - future
2671 GROMACS Task New Normal replace constants like M_PI 12/20/2019 01:17 PM GROMACS - future
2667 GROMACS Feature New Normal Suggested steps for calculating entropy in solution and binding David van der Spoel 03/01/2020 01:35 PM GROMACS - 2020.2
2658 GROMACS Task New Normal Secondary structure assignment via DSSP as native gromacs code Christian Blau 10/09/2018 04:51 PM GROMACS - future
2657 GROMACS Bug New Normal Biphasic tutorial 09/28/2018 10:02 AM
2650 GROMACS Task New Normal revise OpenCL stack recommendations 12/31/2018 11:19 AM GROMACS - future
2649 GROMACS Bug New Normal Virial calculation necessary for correct energy calculation on GPU 12/17/2018 02:32 PM GROMACS - future
2645 GROMACS Bug New Normal Security 09/28/2018 01:16 PM
2644 GROMACS Task New Normal Replace compute_globals Mark Abraham 09/24/2018 05:51 PM GROMACS - future
2628 GROMACS Bug Resolved Normal GMXRC removes trailing colon from existing MANPATH 11/02/2020 11:45 AM
2624 GROMACS Bug New Normal GPU build system not robust enough 09/05/2018 02:00 AM
2621 GROMACS Task New Normal Fine-Grained API to Describe Force Calculation and Neighbourhood Search Prashanth Kanduri 08/22/2018 11:36 AM GROMACS - future
2616 GROMACS Task New Normal Model for MD state 09/14/2018 05:12 PM
2611 GROMACS Bug New Normal issues with gpu_utils-test with GMX_BUILD_UNITTESTS=OFF and on OSX 08/14/2018 07:03 PM
2608 GROMACS Task New Normal Remove code duplication between OpenCL and CUDA 09/24/2018 12:47 PM
2607 GROMACS Bug New Normal Grompp becomes extremely slow when many pull groups are present 08/11/2018 08:54 AM
2606 GROMACS Bug New Normal Free Energy Calculation -- Function type Fourier Dih. Not implemented in ip_pert 08/10/2018 01:48 AM
2603 GROMACS Task New Normal Add ability to properly check coordinate files during testing Paul Bauer 10/15/2018 01:16 PM GROMACS - future
2601 GROMACS Feature New Normal Free energy calculations, soft-core potential Vytautas Gapsys 02/10/2020 11:29 AM GROMACS - future
2598 GROMACS Bug New Normal Tools using read_next_x cannot read TNG files with sanitzers 10/15/2018 01:16 PM GROMACS - future
2596 GROMACS Feature New Normal Constant potential method Benson Muite 05/10/2019 09:54 AM
2595 GROMACS Task New Normal Reusable Utilities for Schedules Prashanth Kanduri 02/22/2019 03:48 PM GROMACS - future
2594 GROMACS Feature New Normal Multi-level GMX API Prashanth Kanduri 02/22/2019 03:48 PM GROMACS - future
2590 GROMACS Task New Normal Essential Dynamics as module providing forces Christian Blau 08/22/2018 05:03 PM GROMACS - future
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
2585 GROMACS Feature Resolved Normal Infrastructure supporting external API 12/11/2019 12:39 PM
2582 GROMACS Bug Blocked, need info Normal Compilation issues with CUDA V9.1.85 and both gcc5 and gcc6 Szilárd Páll 07/23/2018 07:46 PM
2581 GROMACS Feature Accepted Normal User interface for hybrid Monte Carlo 12/20/2019 12:24 PM GROMACS - future
2579 GROMACS Feature New Normal Add dimensionality option to gmx trjconv -center 07/19/2018 04:53 PM GROMACS - future
2576 GROMACS Bug New Normal gmx potential -correct outputs the wrong potential 07/25/2018 02:58 PM
2574 GROMACS Feature New Normal iForceSchedule Abstraction Prashanth Kanduri 03/29/2019 05:20 PM GROMACS - future
2570 GROMACS Feature New Normal Better string formatting and printing 05/02/2019 12:20 PM
2567 GROMACS Bug New Normal make check fails at test 23 SIMD errors 07/10/2018 09:35 AM
2564 GROMACS Bug New Normal Result Summary Different For Jobs With Different Numbers of Nodes 07/05/2018 02:39 PM
2563 GROMACS Bug New Normal Windows 7 Compilation with GPU support 07/02/2018 09:58 AM
2556 GROMACS Feature New Normal make default selections suitable for DNA and RNA Mark Abraham 06/20/2018 01:48 PM
2546 GROMACS Task New Normal Add more assertions to AWH code Viveca Lindahl 06/06/2018 11:20 AM GROMACS - future
2545 GROMACS Feature New Normal Should grompp fix periodicity of input files? David van der Spoel 10/03/2018 11:32 PM GROMACS - future
2544 GROMACS Bug New Normal gmx rmsf does not fix periodicity in reference structure David van der Spoel 08/21/2018 10:36 AM GROMACS - future
2538 GROMACS Task New Normal organize more of the PME GPU code along task-specific lines Mark Abraham 05/31/2018 05:41 PM
2537 GROMACS Task New Normal Simplify PME solve reduction Aleksei Iupinov 12/20/2019 12:21 PM GROMACS - future
2535 GROMACS Task New Normal consider compiling opencl fft kernels once 05/31/2018 01:33 PM
2532 GROMACS Task New Normal enable queue priorities in OpenCL 05/29/2018 02:29 PM
2530 GROMACS Task New Normal consider using CUDA Driver API 09/23/2018 11:47 PM GROMACS - future
2528 GROMACS Task New Normal PME GPU tuning 12/31/2018 11:18 AM GROMACS - future
2527 GROMACS Task New Normal Rename GpuEventSynchronizer to something more fitting (after mergin PME OpenCL) 10/30/2018 04:06 AM GROMACS - future
2526 GROMACS Bug New Normal Bug of gmx hbond 05/30/2018 03:12 PM
2524 GROMACS Task New Normal struct alignment/packing for OpenCL host & device code 12/20/2019 12:20 PM GROMACS - future
2522 GROMACS Task Resolved Normal OpenCL context duplication 03/11/2020 04:15 PM GROMACS - future
2521 GROMACS Task New Normal Implement alternating PME/NB wait for OpenCL 10/15/2018 12:39 PM
2520 GROMACS Task New Normal Treat OpenCL kernel width more diligently 05/24/2018 06:21 PM
2518 GROMACS Task New Normal redesign task-assignment code for OpenCL 12/20/2019 12:19 PM GROMACS - future
2514 GROMACS Task New Normal PME OpenCL reductions with intrinsics 05/31/2018 12:27 AM GROMACS - future
2513 GROMACS Bug Feedback wanted Normal ref_t and temperature incorrect with coulomb-type = user Yu Du 05/31/2018 04:05 PM
2501 GROMACS Task New Normal Documentation section on log file contents Kevin Boyd 10/03/2018 09:48 PM GROMACS - future
2498 GROMACS Task New Normal OpenCL memory pinning/mapping 12/20/2019 12:18 PM GROMACS - future
2495 GROMACS Task Accepted Normal replace -noconfout with mdp option Mark Abraham 12/28/2019 10:39 AM GROMACS - 2021
2492 GROMACS Task New Normal implement force calculation via ForceProviders containing collections of IForceProvider Mark Abraham 09/19/2018 03:13 PM GROMACS - future
2490 GROMACS Task New Normal evaluate two-step communicators Szilárd Páll 10/03/2018 09:47 PM GROMACS - future
2488 GROMACS Task New Normal use MPI non-blocking collectives to overlap pull comm 04/25/2018 04:19 PM
2482 GROMACS Bug Feedback wanted Normal Atoms/molecules in freezegrps move and system crashes 05/18/2018 07:13 PM
2480 GROMACS Bug New Normal pdb2gmx does not protonate correctly for united-atom Gromos Mark Abraham 12/20/2019 12:17 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
2473 GROMACS Bug New Normal mdrun sometimes stalls due to large coordinates with no constraints 04/04/2018 10:15 PM
2469 GROMACS Task New Normal implement GPU timer reduction for reporting 03/27/2018 05:08 PM
2464 GROMACS Task New Normal GPU performance goals overview 03/26/2018 10:42 AM
2462 GROMACS Task New Normal consider adding STL misuse tests 03/23/2018 01:23 AM
2460 GROMACS Bug New Normal Allow inclusion of user libraries through CMake cache variables 03/28/2018 08:47 PM
2456 GROMACS Task New Normal Add a pull module external potential tests 03/15/2018 03:02 PM
2452 GROMACS Task In Progress Normal Reduce data dependencies in mdrun algorithms Berk Hess 03/14/2018 08:47 PM
2451 GROMACS Feature Resolved Normal Linear virtual sites with fixed distance David van der Spoel 09/16/2019 01:15 PM
2448 GROMACS Task Accepted Normal should mdrun -multidir permit only one directory? 03/21/2018 12:10 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
2442 GROMACS Task New Normal Port gmx saxs and gmx sans to c++ Joe Jordan 06/28/2018 10:06 PM GROMACS - future
2435 GROMACS Task New Normal identify and note about/tune task offload in GPU-bound runs 03/02/2018 04:08 PM
2429 GROMACS Feature New Normal Add option of periodic chain topology to pdb2gmx 03/10/2018 01:01 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
2427 GROMACS Bug New Normal gmx select gives syntax error for selection involving evaluating simple arithmetic expression 02/27/2018 05:15 PM
2426 GROMACS Feature In Progress Normal Trajectory analysis tool for functional mode analysis by partial least squares fitting (PLS-FMA) 10/03/2018 11:31 PM GROMACS - future
2425 GROMACS Task New Normal testing multisim with multiple ranks per simulation Mark Abraham 12/20/2019 12:13 PM GROMACS - 2021
2423 GROMACS Task New Normal modernize constraints code Mark Abraham 09/19/2018 03:01 PM GROMACS - future
2422 GROMACS Task New Normal write C kernel for tables in Verlet scheme 02/26/2018 01:38 PM
2412 GROMACS Task New Normal attempt to do better FFTW planning 03/15/2018 05:01 PM
2402 GROMACS Task New Normal PME kernels general performance improvements 03/26/2018 10:41 AM GROMACS - future
2396 GROMACS Task New Normal Refactor trajectoryanalysis module to allow handling of trajectory frame manipulation Paul Bauer 12/02/2019 01:24 PM GROMACS - 2021-infrastructure-stable
2395 GROMACS Task In Progress Normal break up commrec Mark Abraham 12/15/2019 11:51 AM GROMACS - 2021-infrastructure-stable
2393 GROMACS Bug New Normal incorrect error message with omitted command line flag before its argument 01/24/2018 11:24 PM
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
2383 GROMACS Task New Normal Add JSON interface to write and read files Paul Bauer 01/16/2018 02:01 PM GROMACS - future
2382 GROMACS Task New Normal Simplify Doxygen guidelines 01/13/2018 12:40 AM
2379 GROMACS Task New Normal check leftover FIXMEs in r2018 Szilárd Páll 12/31/2018 11:16 AM GROMACS - future
2376 GROMACS Task New Normal max_mpi_ranks has wrong name 02/10/2018 11:03 AM
2375 GROMACS Task New Normal Clarify execution phases for MD simulation 04/30/2019 12:59 PM
2371 GROMACS Task New Normal mtop searching needs reconsideration 01/04/2018 11:54 AM GROMACS - future
2368 GROMACS Task In Progress Normal update implementation of gmx msd Kevin Boyd 11/03/2018 07:43 PM GROMACS - future
2367 GROMACS Task New Normal construct pbc_simd less often 09/24/2018 11:02 PM GROMACS - future
2354 GROMACS Feature New Normal develop configuration file support for control of task layout 09/19/2018 03:01 PM GROMACS - future
2353 GROMACS Task New Normal improve on relative tolerance for constructing tables 12/20/2019 12:12 PM GROMACS - 2021
2351 GROMACS Task New Normal Avoid the SIMD module depending on non-trivial parts of Gromacs 12/14/2017 02:47 AM GROMACS - future
2304 GROMACS Task New Normal Document and propose tracking mdrun heuristics 10/03/2018 09:39 PM GROMACS - future
2294 GROMACS Task New Normal Require identical hardware on nodes on parallel runs 11/19/2017 08:54 PM
2289 GROMACS Feature New Normal gmx spatial add ability to perform over multiple reference structures 11/08/2017 12:31 AM
2283 GROMACS Feature New Normal Force distribution analysis Bernd Doser 10/27/2017 11:44 AM
2282 GROMACS Feature New Normal Density map toolset Christian Blau 03/21/2019 06:08 PM GROMACS - future
2255 GROMACS Bug New Normal nstlist override stopped affecting the input parameter listing 12/17/2017 08:05 AM
2254 GROMACS Feature Resolved Normal GPU extensions for Google Tests 10/06/2020 12:15 PM
2248 GROMACS Feature New Normal Label all SIMD functions as pure/nodiscard 02/04/2019 04:49 AM
2239 GROMACS Feature New Normal split libgromacs into base and full 01/07/2019 01:47 AM
2238 GROMACS Task In Progress Normal GPU emulation mode support for rolling pruning missing Berk Hess 12/21/2017 03:21 PM
2233 GROMACS Bug Accepted Normal replica exchange and -append bugged? 03/05/2018 01:38 PM
2232 GROMACS Bug New Normal pdb2gmx can't form special bonds with terminal patched atoms 12/03/2017 01:35 PM
2231 GROMACS Bug New Normal convert-tpr aborts when saving subset of the system 01/12/2018 03:52 PM
2226 GROMACS Feature New Normal Harmonise commands for exit in make_ndx and distance 08/04/2017 12:24 PM
2224 GROMACS Feature New Normal Proposed feature: conditional stop Vedran Miletic 12/20/2019 12:11 PM GROMACS - 2021
2221 GROMACS Task New Normal Avoid preprocessor for SIMD functions 02/21/2018 01:43 PM
2220 GROMACS Feature New Normal report relevant env var behaviour to console 07/31/2017 09:40 PM
2218 GROMACS Feature Feedback wanted Normal A tiny feature: damping for umbrella pull 08/16/2017 07:20 PM
2216 GROMACS Task New Normal GROMACS SIMD acceleration: generation 3 Erik Lindahl 07/17/2017 06:57 PM GROMACS - future
2208 GROMACS Bug New Normal cuFFT linking 06/30/2017 01:58 PM
2207 GROMACS Feature New Normal solvent excluded volume of large molecule with periodic boundary condition 06/16/2017 10:37 AM
2185 GROMACS Task New Normal add docs on MPI + CUDA w/wo MPS 05/24/2017 05:17 PM
2178 GROMACS Task New Normal Move checks for specific warnings to source repo 05/12/2017 03:57 PM
2175 GROMACS Task New Normal improve clang static analyzer docs further 01/04/2018 04:13 PM GROMACS - future
2169 GROMACS Task New Normal remove 'continuation' mdp option 12/29/2019 10:31 AM GROMACS - 2021
2168 GROMACS Task Feedback wanted Normal Design for multiple comparisons against same test reference data 05/08/2017 02:45 PM GROMACS - future
2166 GROMACS Task Accepted Normal gmx trjconv functionality should check for mismatch between the tpr and the trajectory 05/05/2017 04:32 PM
2158 GROMACS Task New Normal consider adding post-submit test that runs PME with 2xNN kernels 04/19/2017 08:04 PM
2147 GROMACS Bug Feedback wanted Normal Parrinello-Rahman barostat not properly working 06/06/2017 07:53 AM
2139 GROMACS Feature New Normal More precise/explicit documentation conventions 01/07/2018 11:54 PM
2137 GROMACS Feature New Normal Preliminary refactoring of constraints and update machinery. Michael Shirts 03/11/2017 08:32 AM GROMACS - future
2132 GROMACS Feature New Normal Intermediate code for xvg handling 03/08/2017 05:12 PM GROMACS - future
2126 GROMACS Feature New Normal implement native CUDA support in CMake 10/29/2019 09:03 PM
2115 GROMACS Task New Normal trjconv does too many things, and combinations of them work poorly 10/02/2018 09:04 AM
2113 GROMACS Bug New Normal Google tests and execution order 03/05/2018 02:05 PM
2111 GROMACS Feature In Progress Normal Implement Gaussian screening of electrostatics 02/23/2019 12:33 PM
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
2092 GROMACS Task New Normal Tests running on GPU, and hardware assignment 12/19/2017 05:27 PM GROMACS - future
2090 GROMACS Feature New Normal redirecting stdout or stderr for testing Mark Abraham 12/15/2016 03:15 AM
2089 GROMACS Task New Normal Encourage code review 01/10/2017 12:03 AM
2080 GROMACS Feature New Normal add grompp warning for suitableness for domain decomposition 11/23/2016 03:03 PM
2070 GROMACS Feature In Progress Normal Physical validation testing Michael Shirts 01/03/2020 09:36 PM GROMACS - future
2068 GROMACS Feature New Normal Access to low level classes 03/02/2019 01:37 AM GROMACS - future
2065 GROMACS Bug New Normal thread-MPI internal errors 11/08/2018 03:43 PM
2060 GROMACS Feature New Normal Convert enum to enum class 10/17/2016 05:27 PM
2059 GROMACS Task In Progress Normal Separate different types of data in t_state 12/27/2019 04:42 PM GROMACS - 2021
2053 GROMACS Task New Normal refine notation in GPU code 12/20/2019 01:04 PM GROMACS - 2021
2048 GROMACS Task New Normal C++11: CUDA dependency on general headers 09/07/2016 10:30 PM
2045 GROMACS Task New Normal API design and language bindings Peter Kasson 01/29/2020 03:59 PM
2039 GROMACS Bug New Normal mdrun -pinstride defaults are too confusing 12/13/2017 04:14 AM
2035 GROMACS Task New Normal A common trajectory analysis data exchange format 03/15/2017 05:46 PM GROMACS - future
2034 GROMACS Feature New Normal Unit tests for bonded forces David van der Spoel 06/29/2019 10:22 AM GROMACS - future
2020 GROMACS Bug New Normal Possible issue with md-vv integrator Mark Abraham 03/11/2017 08:30 AM
2018 GROMACS Feature New Normal Pulling along a line between given points 07/27/2016 09:59 AM
2017 GROMACS Task In Progress Normal Modularize simulation option storage and reading from mdp files Christian Blau 04/06/2018 06:07 PM GROMACS - future
2015 GROMACS Feature New Normal Auto recovery from dd communication error 07/28/2016 03:17 PM
2010 GROMACS Task New Normal Use size_t instead of int for indexing 07/01/2018 07:57 AM
2009 GROMACS Task New Normal improve command-line reporting of useful things 07/26/2016 12:54 PM
2005 GROMACS Feature New Normal Full Correlation Analysis (FCA) as Trajectory Analysis Module Christian Blau 02/07/2018 02:19 PM GROMACS - future
2003 GROMACS Task New Normal reconsider various simd flags 07/07/2016 11:23 PM
2001 GROMACS Feature New Normal add MPI info to the mdrun log header 07/06/2016 05:21 PM
1974 GROMACS Feature New Normal Report atom numbers and types in the error message about missed parameters 05/30/2016 09:24 AM
1973 GROMACS Task New Normal OpenCL implementation wish list 05/27/2016 03:42 PM
1972 GROMACS Feature New Normal external potential modules for refinement against experimental data 08/22/2018 05:03 PM GROMACS - future
1971 GROMACS Task New Normal Removing buggy features vs. keeping workflows 01/19/2018 01:36 PM GROMACS - future
1964 GROMACS Feature Accepted Normal "pull=no" should not produce warnings about "unknown" pull keywords 05/20/2016 02:37 PM
1947 GROMACS Task New Normal Consider fixing corner case in TinyXML2 Mark Abraham 04/19/2016 01:40 AM
1936 GROMACS Task New Normal treat default-able mdp fields as strings 04/02/2016 10:32 PM GROMACS - future
1934 GROMACS Bug New Normal QMMM with ORCA: memory leaks, buffer overflows and much more 07/10/2016 09:26 AM
1925 GROMACS Task In Progress Normal remove concept of unilateral global communication 12/29/2019 10:35 AM GROMACS - 2021
1919 GROMACS Bug Accepted Normal static linking issues cause by hwloc support 10/12/2018 10:49 PM GROMACS - future
1900 GROMACS Feature New Normal Implement some new errors in grompp 06/22/2016 05:20 PM
1885 GROMACS Feature New Normal DPD Thermostat 01/26/2016 10:17 AM
1880 GROMACS Bug Feedback wanted Normal PP-PME load balancing issue Berk Hess 10/03/2018 09:45 PM GROMACS - future
1876 GROMACS Task New Normal Reorganize vector input passed to core MD routines 06/01/2016 01:59 PM GROMACS - future
1867 GROMACS Feature New Normal make coupling implementations reversible 12/02/2015 07:43 AM
1864 GROMACS Feature New Normal write tng files with energies Magnus Lundborg 07/11/2016 08:00 PM
1862 GROMACS Task New Normal Fully replace t_topology by gmx_mtop_t 02/13/2019 04:53 PM
1855 GROMACS Task New Normal Convert preprocessor use so that symbols are always defined 06/28/2016 02:17 PM
1854 GROMACS Feature New Normal Remove all cyclic dependencies 05/25/2017 08:34 AM
1852 GROMACS Task New Normal Remove group scheme 03/03/2020 09:03 PM GROMACS - future
1849 GROMACS Feature New Normal expanded ensemble -- Adaptive Integration Method Christopher Mirabzadeh 07/11/2016 08:01 PM
1843 GROMACS Bug In Progress Normal pbc=xy with 2 walls floating point exception with the verlet scheme Berk Hess 10/31/2016 11:35 AM
1842 GROMACS Feature New Normal Replace XML with JSON 01/18/2018 05:12 PM
1829 GROMACS Task New Normal Future of thread level parallelism 11/18/2016 05:29 PM
1828 GROMACS Task New Normal Exception handling in mdrun 10/07/2015 11:36 AM
1826 GROMACS Task New Normal investigate non-optimal results with CPU-GPU balancing on AMD Szilárd Páll 12/20/2019 12:04 PM GROMACS - future
1811 GROMACS Bug New Normal Extrae build issues 12/13/2017 03:43 AM
1793 GROMACS Task New Normal cleanup of integration loop Mark Abraham 10/31/2018 10:49 PM GROMACS - future
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