Commits · REDS · Christopher Summa / GROMACS · GitLab

Jan 07, 2021
- added new REDS-specific variable to allow very verbose energy output in... · 400a4b34
  Christopher Summa authored Jan 07, 2021
  400a4b34
Oct 08, 2020
- made a small change to md.cpp that was causing a segfault in vanilla GROMACS,... · 55eba0b6
  Christopher Summa authored Oct 08, 2020
  55eba0b6
Oct 07, 2020
- in fileio/tpxio.cpp, moved a REDS-specific line of output into a conditional,... · 921b3dc2
  Christopher Summa authored Oct 07, 2020
  921b3dc2
Jul 14, 2020
- last commit broke something with scaling of the valume and pressure - the... · 95bd323d
  Christopher Summa authored Jul 14, 2020
  95bd323d
Jul 08, 2020
- Steve discovered that where were modifying zeta, and outputting the energies,... · a8efda72
  Christopher Summa authored Jul 08, 2020
  a8efda72
May 20, 2020
- modified output in updateZeta so that the zeta output in the scaled replicas... · 8283c0a0
  Christopher Summa authored May 20, 2020
  8283c0a0
- confirmed that zetas are exchanging correctly - put a bunch of debug output... · 01f2e3c6
  Christopher Summa authored May 19, 2020
  01f2e3c6
May 19, 2020
- fixed the output of final zeta values in each replica's md.log file · 366cd812
  Christopher Summa authored May 19, 2020
  366cd812
May 11, 2020
- working on getting REDS zeta values to be set via the input mdp files. not quite working yet · ba3f0bf8
  Christopher Summa authored May 11, 2020
  ba3f0bf8
May 05, 2020
- put some output we used for debugging behind the REDS_DEBUG compiler flag · b4460936
  Christopher Summa authored May 05, 2020
  b4460936
May 02, 2020
- added a dependence on bCalcEner for entrance into the updateZeta method of the REDS code · 0e4dbb33
  Christopher Summa authored May 02, 2020
  0e4dbb33
May 01, 2020
- removed remaining two references to REDS_preprod as it has become unnecessary · 115e8495
  Christopher Summa authored May 01, 2020
  115e8495
Apr 30, 2020
- got rid of some unnecessary output, deleted the REDS preprod-specific code and... · 586c6a91
  Christopher Summa authored Apr 30, 2020
  586c6a91
Apr 27, 2020
- commented out code that was no longer necessary in REDS code (unused... · 7782cf84
  Christopher Summa authored Apr 27, 2020
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- updated md.cpp to do scaling and unscaling of pressures (and produce lots of... · aa2d549a
  Christopher Summa authored Apr 27, 2020
  aa2d549a
Apr 24, 2020
- updated tpxio so it only produces output on values of REDS specific variables... · 3818b8c7
  Christopher Summa authored Apr 24, 2020
  3818b8c7
Apr 23, 2020
- updated methods that do scaling in REDS specific code to accept betaLeft and... · 4124eb61
  Christopher Summa authored Apr 23, 2020
  4124eb61
- added machinery for two new REDS-specific varables - betaLeft_reds and betaRight_reds · c341625f
  Christopher Summa authored Apr 23, 2020
  c341625f
Apr 20, 2020
- began laying the groundwork for being able to input starting zeta values, and... · ff4122f3
  Christopher Summa authored Apr 20, 2020
  ff4122f3
Apr 07, 2020
- fixed an operator bug in the calculation of the the biasing function - in the... · 0c33b84d
  Christopher Summa authored Apr 07, 2020
  0c33b84d
Mar 13, 2020
- making modifications to the mdrun and replicaexchange methods to test that... · 54ac7f7c
  Christopher Summa authored Mar 13, 2020
  54ac7f7c
Feb 18, 2020
- removed call the updateZeta_REDS_preprod - because the optimization scripts... · 64c65a8a
  Christopher Summa authored Feb 17, 2020
  64c65a8a
Feb 17, 2020
- modified preproduction version of updateZeta so that it only pegs zeta around... · 5a951568
  Christopher Summa authored Feb 17, 2020
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- added a preproduction specific variant of updateZeta that pegs zeta at a value near 0.5 · bd4446c6
  Christopher Summa authored Feb 17, 2020
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- added first version of code for REDS (replica exhange with dynamical scaling) · f15e7dcc
  Christopher Summa authored Feb 17, 2020
  f15e7dcc
Dec 09, 2019
- fixed typo in comment for REDS B parameter in inputrec.h · 6ac6fd55
  Christopher Summa authored Dec 09, 2019
  6ac6fd55
Dec 05, 2019
- modified src/gromacs/fileio/tpxio.cpp so that REDS-specific parameters can be... · fe63722a
  Christopher Summa authored Dec 05, 2019
  fe63722a
- added code in src/gromacs/mdtypes/inputrec.h and... · ceb67e21
  Christopher Summa authored Dec 05, 2019
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- added zeta value, needed for REDS, to the state struct, and two · d58cb3ce
  Christopher Summa authored Dec 05, 2019
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Nov 28, 2019
- Remove assertion failure in AWH without initial stage · 6dd2746d
  Berk Hess authored Nov 28, 2019
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Nov 26, 2019
- Fix issues with AWH with periodic pulling · 14daed33
  Berk Hess authored Nov 25, 2019 and Paul Bauer committed Nov 26, 2019
  14daed33
Nov 25, 2019
- Fix duplicate CONNECT records in pdb files · 7d142404
  Christian Blau authored Nov 25, 2019 and Paul Bauer committed Nov 25, 2019
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Nov 18, 2019
- Fix intermolecular interactions with DD · 2f99f9a6
  Berk Hess authored Nov 18, 2019
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Nov 07, 2019
- Fix .gro large box writing · 0a698f15
  Berk Hess authored Nov 05, 2019
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Nov 06, 2019
- Work around broken Apple compilers in Mac OS 10.15 · 2d92af68
  Erik Lindahl authored Nov 06, 2019
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Oct 23, 2019
- Fix illegal memory access in FE calculations · c26b330a
  Berk Hess authored Oct 23, 2019
  c26b330a
Oct 09, 2019
- Increase spc minimization test tolerance · 404259bc
  Berk Hess authored Sep 29, 2019 and Paul Bauer committed Oct 09, 2019
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- Fix harmless OpenMP write race · 05b4e2b4
  Berk Hess authored Oct 02, 2019
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- Fix GPU atom data init timer issue · 10d41a6e
  Berk Hess authored Oct 02, 2019
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- Fix random energy and virial with PME on GPU on a PME-only rank · 54898ee5
  Berk Hess authored Oct 04, 2019 and Paul Bauer committed Oct 09, 2019
  54898ee5