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(parent: ea20c5f) | patch
Make it possible to use FEP lambda states as a reaction coordinate in AWH. Atom masse...
authorMagnus Lundborg <magnus.lundborg@scilifelab.se>
Thu, 20 Aug 2020 12:15:28 +0000 (12:15 +0000)
committerMagnus Lundborg <magnus.lundborg@scilifelab.se>
Thu, 20 Aug 2020 12:15:28 +0000 (12:15 +0000)
commit176671b9dcd6975f55a4e70a244f4d962db2d9f5
tree025352ea070a3b093e5c139fa17a501a58ce7232tree | snapshot
parentea20c5f09c1e12ebb50a7a1f969d752326351f39commit | diff
Make it possible to use FEP lambda states as a reaction coordinate in AWH. Atom masses and constraints cannot be perturbed (yet). It is possible to use a multidimensional bias where the lambda state is one dimension. An AWH FEP lambda state dimension is always using a discrete Gibbs sampler (umbrella), even if another dimension is using a convolved bias potential.
48 files changed:
docs/reference-manual/special/awh.rst diff | blob | history
docs/release-notes/2021/major/features.rst diff | blob | history
docs/user-guide/mdp-options.rst diff | blob | history
src/gromacs/awh/awh.cpp diff | blob | history
src/gromacs/awh/awh.h diff | blob | history
src/gromacs/awh/bias.cpp diff | blob | history
src/gromacs/awh/bias.h diff | blob | history
src/gromacs/awh/biasgrid.cpp diff | blob | history
src/gromacs/awh/biasgrid.h diff | blob | history
src/gromacs/awh/biasparams.cpp diff | blob | history
src/gromacs/awh/biasparams.h diff | blob | history
src/gromacs/awh/biasstate.cpp diff | blob | history
src/gromacs/awh/biasstate.h diff | blob | history
src/gromacs/awh/coordstate.cpp diff | blob | history
src/gromacs/awh/coordstate.h diff | blob | history
src/gromacs/awh/dimparams.h diff | blob | history
src/gromacs/awh/pointstate.cpp diff | blob | history
src/gromacs/awh/pointstate.h diff | blob | history
src/gromacs/awh/read_params.cpp diff | blob | history
src/gromacs/awh/read_params.h diff | blob | history
src/gromacs/awh/tests/CMakeLists.txt diff | blob | history
src/gromacs/awh/tests/bias.cpp diff | blob | history
src/gromacs/awh/tests/bias_fep_lambda_state.cpp [new file with mode: 0644] blob
src/gromacs/awh/tests/biasstate.cpp diff | blob | history
src/gromacs/awh/tests/refdata/WithParameters_BiasFepLambdaStateTest_ForcesBiasPmf_0.xml [new file with mode: 0644] blob
src/gromacs/awh/tests/refdata/WithParameters_BiasFepLambdaStateTest_ForcesBiasPmf_1.xml [new file with mode: 0644] blob
src/gromacs/awh/tests/refdata/WithParameters_BiasFepLambdaStateTest_ForcesBiasPmf_2.xml [new file with mode: 0644] blob
src/gromacs/awh/tests/refdata/WithParameters_BiasFepLambdaStateTest_ForcesBiasPmf_3.xml [new file with mode: 0644] blob
src/gromacs/awh/tests/refdata/WithParameters_BiasFepLambdaStateTest_ForcesBiasPmf_4.xml [new file with mode: 0644] blob
src/gromacs/awh/tests/refdata/WithParameters_BiasFepLambdaStateTest_ForcesBiasPmf_5.xml [new file with mode: 0644] blob
src/gromacs/awh/tests/refdata/WithParameters_BiasFepLambdaStateTest_ForcesBiasPmf_6.xml [new file with mode: 0644] blob
src/gromacs/awh/tests/refdata/WithParameters_BiasFepLambdaStateTest_ForcesBiasPmf_7.xml [new file with mode: 0644] blob
src/gromacs/awh/tests/refdata/WithParameters_BiasTest_ForcesBiasPmf_0.xml diff | blob | history
src/gromacs/awh/tests/refdata/WithParameters_BiasTest_ForcesBiasPmf_1.xml diff | blob | history
src/gromacs/awh/tests/refdata/WithParameters_BiasTest_ForcesBiasPmf_2.xml diff | blob | history
src/gromacs/awh/tests/refdata/WithParameters_BiasTest_ForcesBiasPmf_3.xml diff | blob | history
src/gromacs/awh/tests/refdata/WithParameters_BiasTest_ForcesBiasPmf_4.xml diff | blob | history
src/gromacs/awh/tests/refdata/WithParameters_BiasTest_ForcesBiasPmf_5.xml diff | blob | history
src/gromacs/awh/tests/refdata/WithParameters_BiasTest_ForcesBiasPmf_6.xml diff | blob | history
src/gromacs/awh/tests/refdata/WithParameters_BiasTest_ForcesBiasPmf_7.xml diff | blob | history
src/gromacs/gmxana/gmx_awh.cpp diff | blob | history
src/gromacs/gmxpreprocess/grompp.cpp diff | blob | history
src/gromacs/gmxpreprocess/readir.cpp diff | blob | history
src/gromacs/mdlib/enerdata_utils.cpp diff | blob | history
src/gromacs/mdlib/sim_util.cpp diff | blob | history
src/gromacs/mdrun/md.cpp diff | blob | history
src/gromacs/mdtypes/awh_params.h diff | blob | history
src/gromacs/mdtypes/enerdata.h diff | blob | history
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