Yuri Victorovich
660 lines
28 KiB
Plaintext
660 lines
28 KiB
Plaintext
bin/plumed
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bin/plumed-config
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bin/plumed-patch
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include/plumed/asmjit/arch.h
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include/plumed/asmjit/arm.h
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include/plumed/asmjit/asmjit.h
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include/plumed/asmjit/asmjit_apibegin.h
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include/plumed/asmjit/asmjit_apiend.h
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include/plumed/asmjit/asmjit_build.h
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include/plumed/asmjit/assembler.h
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include/plumed/asmjit/base.h
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include/plumed/asmjit/codebuilder.h
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include/plumed/asmjit/codecompiler.h
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include/plumed/asmjit/codeemitter.h
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include/plumed/asmjit/codeholder.h
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include/plumed/asmjit/constpool.h
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include/plumed/asmjit/cpuinfo.h
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include/plumed/asmjit/func.h
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include/plumed/asmjit/globals.h
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include/plumed/asmjit/inst.h
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include/plumed/asmjit/logging.h
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include/plumed/asmjit/misc_p.h
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include/plumed/asmjit/moved_string.h
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include/plumed/asmjit/operand.h
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include/plumed/asmjit/osutils.h
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include/plumed/asmjit/regalloc_p.h
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include/plumed/asmjit/runtime.h
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include/plumed/asmjit/simdtypes.h
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include/plumed/asmjit/utils.h
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include/plumed/asmjit/vmem.h
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include/plumed/asmjit/x86.h
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include/plumed/asmjit/x86assembler.h
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include/plumed/asmjit/x86builder.h
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include/plumed/asmjit/x86compiler.h
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include/plumed/asmjit/x86emitter.h
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include/plumed/asmjit/x86globals.h
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include/plumed/asmjit/x86inst.h
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include/plumed/asmjit/x86instimpl_p.h
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include/plumed/asmjit/x86internal_p.h
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include/plumed/asmjit/x86logging_p.h
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include/plumed/asmjit/x86misc.h
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include/plumed/asmjit/x86operand.h
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include/plumed/asmjit/x86regalloc_p.h
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include/plumed/asmjit/zone.h
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include/plumed/bias/Bias.h
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include/plumed/bias/ReweightBase.h
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include/plumed/blas/blas.h
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include/plumed/blas/def_external.h
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include/plumed/blas/def_internal.h
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include/plumed/blas/real.h
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include/plumed/cltools/CLTool.h
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include/plumed/colvar/Colvar.h
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include/plumed/colvar/ColvarShortcut.h
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include/plumed/colvar/CoordinationBase.h
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include/plumed/colvar/MultiColvarTemplate.h
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include/plumed/colvar/PathMSDBase.h
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include/plumed/colvar/RMSDVector.h
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include/plumed/config/Config.h
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include/plumed/config/version.h
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include/plumed/core/Action.h
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include/plumed/core/ActionAnyorder.h
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include/plumed/core/ActionAtomistic.h
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include/plumed/core/ActionForInterface.h
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include/plumed/core/ActionPilot.h
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include/plumed/core/ActionRegister.h
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include/plumed/core/ActionSet.h
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include/plumed/core/ActionSetup.h
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include/plumed/core/ActionShortcut.h
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include/plumed/core/ActionToGetData.h
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include/plumed/core/ActionToPutData.h
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include/plumed/core/ActionWithArguments.h
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include/plumed/core/ActionWithMatrix.h
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include/plumed/core/ActionWithValue.h
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include/plumed/core/ActionWithVector.h
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include/plumed/core/ActionWithVirtualAtom.h
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include/plumed/core/CLTool.h
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include/plumed/core/CLToolMain.h
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include/plumed/core/CLToolRegister.h
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include/plumed/core/Colvar.h
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include/plumed/core/DataPassingObject.h
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include/plumed/core/DataPassingTools.h
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include/plumed/core/DomainDecomposition.h
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include/plumed/core/ExchangePatterns.h
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include/plumed/core/FlexibleBin.h
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include/plumed/core/GREX.h
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include/plumed/core/GenericMolInfo.h
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include/plumed/core/Group.h
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include/plumed/core/ModuleMap.h
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include/plumed/core/PbcAction.h
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include/plumed/core/PlumedMain.h
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include/plumed/core/PlumedMainInitializer.h
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include/plumed/core/RegisterBase.h
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include/plumed/core/TargetDist.h
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include/plumed/core/Value.h
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include/plumed/core/WithCmd.h
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include/plumed/function/Between.h
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include/plumed/function/Combine.h
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include/plumed/function/Custom.h
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include/plumed/function/Function.h
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include/plumed/function/FunctionOfMatrix.h
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include/plumed/function/FunctionOfScalar.h
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include/plumed/function/FunctionOfVector.h
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include/plumed/function/FunctionShortcut.h
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include/plumed/function/FunctionTemplateBase.h
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include/plumed/function/LessThan.h
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include/plumed/function/MoreThan.h
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include/plumed/function/Sum.h
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include/plumed/gridtools/ActionWithGrid.h
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include/plumed/gridtools/EvaluateGridFunction.h
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include/plumed/gridtools/FunctionOfGrid.h
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include/plumed/gridtools/GridCoordinatesObject.h
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include/plumed/gridtools/GridSearch.h
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include/plumed/gridtools/Interpolator.h
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include/plumed/gridtools/RDF.h
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include/plumed/isdb/MetainferenceBase.h
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include/plumed/lapack/def_external.h
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include/plumed/lapack/def_internal.h
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include/plumed/lapack/lapack.h
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include/plumed/lapack/lapack_limits.h
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include/plumed/lapack/real.h
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include/plumed/lepton/CompiledExpression.h
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include/plumed/lepton/CustomFunction.h
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include/plumed/lepton/Exception.h
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include/plumed/lepton/ExpressionProgram.h
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include/plumed/lepton/ExpressionTreeNode.h
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include/plumed/lepton/Lepton.h
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include/plumed/lepton/MSVC_erfc.h
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include/plumed/lepton/Operation.h
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include/plumed/lepton/ParsedExpression.h
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include/plumed/lepton/Parser.h
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include/plumed/lepton/windowsIncludes.h
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include/plumed/matrixtools/MatrixOperationBase.h
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include/plumed/molfile/Gromacs.h
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include/plumed/molfile/endianswap.h
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include/plumed/molfile/fastio.h
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include/plumed/molfile/largefiles.h
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include/plumed/molfile/libmolfile_plugin.h
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include/plumed/molfile/molfile_plugin.h
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include/plumed/molfile/periodic_table.h
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include/plumed/molfile/readpdb.h
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include/plumed/molfile/vmdplugin.h
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include/plumed/multicolvar/MultiColvarShortcuts.h
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include/plumed/secondarystructure/SecondaryStructureRMSD.h
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include/plumed/setup/ActionSetup.h
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include/plumed/small_vector/small_vector.h
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include/plumed/tools/Angle.h
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include/plumed/tools/AtomNumber.h
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include/plumed/tools/BiasRepresentation.h
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include/plumed/tools/Brent1DRootSearch.h
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include/plumed/tools/CheckInRange.h
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include/plumed/tools/Citations.h
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include/plumed/tools/Communicator.h
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include/plumed/tools/ConjugateGradient.h
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include/plumed/tools/DLLoader.h
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include/plumed/tools/ERMSD.h
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include/plumed/tools/Exception.h
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include/plumed/tools/File.h
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include/plumed/tools/FileBase.h
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include/plumed/tools/ForwardDecl.h
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include/plumed/tools/Grid.h
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include/plumed/tools/HistogramBead.h
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include/plumed/tools/IFile.h
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include/plumed/tools/KernelFunctions.h
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include/plumed/tools/Keywords.h
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include/plumed/tools/LatticeReduction.h
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include/plumed/tools/LeptonCall.h
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include/plumed/tools/LinkCells.h
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include/plumed/tools/Log.h
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include/plumed/tools/LoopUnroller.h
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include/plumed/tools/Matrix.h
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include/plumed/tools/MatrixSquareBracketsAccess.h
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include/plumed/tools/MergeVectorTools.h
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include/plumed/tools/Minimise1DBrent.h
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include/plumed/tools/MinimiseBase.h
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include/plumed/tools/MolDataClass.h
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include/plumed/tools/MultiValue.h
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include/plumed/tools/NeighborList.h
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include/plumed/tools/OFile.h
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include/plumed/tools/OpenMP.h
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include/plumed/tools/PDB.h
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include/plumed/tools/Pbc.h
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include/plumed/tools/PlumedHandle.h
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include/plumed/tools/RMSD.h
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include/plumed/tools/Random.h
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include/plumed/tools/RootFindingBase.h
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include/plumed/tools/Stopwatch.h
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include/plumed/tools/Subprocess.h
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include/plumed/tools/SwitchingFunction.h
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include/plumed/tools/Tensor.h
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include/plumed/tools/Tools.h
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include/plumed/tools/Torsion.h
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include/plumed/tools/Tree.h
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include/plumed/tools/TypesafePtr.h
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include/plumed/tools/Units.h
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include/plumed/tools/Vector.h
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include/plumed/tools/h36.h
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include/plumed/vatom/ActionWithVirtualAtom.h
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include/plumed/wrapper/Plumed.h
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include/plumed/xdrfile/xdrfile.h
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include/plumed/xdrfile/xdrfile_trr.h
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include/plumed/xdrfile/xdrfile_xtc.h
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lib/libplumed.a
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lib/libplumed.so
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lib/libplumedKernel.so
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lib/libplumedWrapper.a
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lib/plumed/fortran/plumed.f90
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lib/plumed/fortran/plumed_f08.f90
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lib/plumed/json/syntax.json
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lib/plumed/modulefile
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lib/plumed/patches/gromacs-2022.5.config
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lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/CMakeLists.txt
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lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/CMakeLists.txt.preplumed
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lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/mdlib/expanded.cpp
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lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/mdlib/expanded.cpp.preplumed
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lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/mdlib/expanded.h
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lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/mdlib/expanded.h.preplumed
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lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/mdlib/sim_util.cpp
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lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/mdlib/sim_util.cpp.preplumed
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lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/mdrun/legacymdrunoptions.cpp
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lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/mdrun/legacymdrunoptions.cpp.preplumed
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lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/mdrun/legacymdrunoptions.h
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lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/mdrun/legacymdrunoptions.h.preplumed
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lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/mdrun/md.cpp
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lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/mdrun/md.cpp.preplumed
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lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/mdrun/minimize.cpp
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lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/mdrun/minimize.cpp.preplumed
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lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/mdrun/replicaexchange.cpp
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lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/mdrun/replicaexchange.cpp.preplumed
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lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/mdrun/replicaexchange.h
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lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/mdrun/replicaexchange.h.preplumed
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lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/mdrun/rerun.cpp
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lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/mdrun/rerun.cpp.preplumed
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lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/mdrun/runner.cpp
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lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/mdrun/runner.cpp.preplumed
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lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/modularsimulator/expandedensembleelement.cpp
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lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/modularsimulator/expandedensembleelement.cpp.preplumed
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lib/plumed/patches/gromacs-2023.5.config
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lib/plumed/patches/gromacs-2023.5.diff/src/gromacs/CMakeLists.txt
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lib/plumed/patches/gromacs-2023.5.diff/src/gromacs/CMakeLists.txt.preplumed
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lib/plumed/patches/gromacs-2023.5.diff/src/gromacs/mdlib/expanded.cpp
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lib/plumed/patches/gromacs-2023.5.diff/src/gromacs/mdlib/expanded.cpp.preplumed
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lib/plumed/patches/gromacs-2023.5.diff/src/gromacs/mdlib/expanded.h
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lib/plumed/patches/gromacs-2023.5.diff/src/gromacs/mdlib/expanded.h.preplumed
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lib/plumed/patches/gromacs-2023.5.diff/src/gromacs/mdlib/sim_util.cpp
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lib/plumed/patches/gromacs-2023.5.diff/src/gromacs/mdlib/sim_util.cpp.preplumed
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lib/plumed/patches/gromacs-2023.5.diff/src/gromacs/mdrun/legacymdrunoptions.cpp
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lib/plumed/patches/gromacs-2023.5.diff/src/gromacs/mdrun/legacymdrunoptions.cpp.preplumed
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lib/plumed/patches/gromacs-2023.5.diff/src/gromacs/mdrun/legacymdrunoptions.h
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lib/plumed/patches/gromacs-2023.5.diff/src/gromacs/mdrun/legacymdrunoptions.h.preplumed
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lib/plumed/patches/gromacs-2023.5.diff/src/gromacs/mdrun/md.cpp
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lib/plumed/patches/gromacs-2023.5.diff/src/gromacs/mdrun/md.cpp.preplumed
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lib/plumed/patches/gromacs-2023.5.diff/src/gromacs/mdrun/minimize.cpp
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lib/plumed/patches/gromacs-2023.5.diff/src/gromacs/mdrun/minimize.cpp.preplumed
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lib/plumed/patches/gromacs-2023.5.diff/src/gromacs/mdrun/replicaexchange.cpp
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lib/plumed/patches/gromacs-2023.5.diff/src/gromacs/mdrun/replicaexchange.cpp.preplumed
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lib/plumed/patches/gromacs-2023.5.diff/src/gromacs/mdrun/replicaexchange.h
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lib/plumed/patches/gromacs-2023.5.diff/src/gromacs/mdrun/replicaexchange.h.preplumed
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lib/plumed/patches/gromacs-2023.5.diff/src/gromacs/mdrun/rerun.cpp
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lib/plumed/patches/gromacs-2023.5.diff/src/gromacs/mdrun/rerun.cpp.preplumed
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lib/plumed/patches/gromacs-2023.5.diff/src/gromacs/mdrun/runner.cpp
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lib/plumed/patches/gromacs-2023.5.diff/src/gromacs/mdrun/runner.cpp.preplumed
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lib/plumed/patches/gromacs-2023.5.diff/src/gromacs/modularsimulator/expandedensembleelement.cpp
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lib/plumed/patches/gromacs-2023.5.diff/src/gromacs/modularsimulator/expandedensembleelement.cpp.preplumed
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lib/plumed/patches/gromacs-2023.5.diff/src/gromacs/taskassignment/decidegpuusage.cpp
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lib/plumed/patches/gromacs-2023.5.diff/src/gromacs/taskassignment/decidegpuusage.cpp.preplumed
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lib/plumed/patches/gromacs-2023.5.diff/src/gromacs/taskassignment/include/gromacs/taskassignment/decidegpuusage.h
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lib/plumed/patches/gromacs-2023.5.diff/src/gromacs/taskassignment/include/gromacs/taskassignment/decidegpuusage.h.preplumed
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lib/plumed/patches/gromacs-2024.3.config
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lib/plumed/patches/gromacs-2024.3.diff/src/gromacs/CMakeLists.txt
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lib/plumed/patches/gromacs-2024.3.diff/src/gromacs/CMakeLists.txt.preplumed
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lib/plumed/patches/gromacs-2024.3.diff/src/gromacs/mdlib/expanded.cpp
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lib/plumed/patches/gromacs-2024.3.diff/src/gromacs/mdlib/expanded.cpp.preplumed
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lib/plumed/patches/gromacs-2024.3.diff/src/gromacs/mdlib/expanded.h
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lib/plumed/patches/gromacs-2024.3.diff/src/gromacs/mdlib/expanded.h.preplumed
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lib/plumed/patches/gromacs-2024.3.diff/src/gromacs/mdlib/sim_util.cpp
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lib/plumed/patches/gromacs-2024.3.diff/src/gromacs/mdlib/sim_util.cpp.preplumed
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lib/plumed/patches/gromacs-2024.3.diff/src/gromacs/mdrun/legacymdrunoptions.cpp
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lib/plumed/patches/gromacs-2024.3.diff/src/gromacs/mdrun/legacymdrunoptions.cpp.preplumed
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lib/plumed/patches/gromacs-2024.3.diff/src/gromacs/mdrun/legacymdrunoptions.h
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lib/plumed/patches/gromacs-2024.3.diff/src/gromacs/mdrun/legacymdrunoptions.h.preplumed
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lib/plumed/patches/gromacs-2024.3.diff/src/gromacs/mdrun/md.cpp
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lib/plumed/patches/gromacs-2024.3.diff/src/gromacs/mdrun/md.cpp.preplumed
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lib/plumed/patches/gromacs-2024.3.diff/src/gromacs/mdrun/minimize.cpp
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lib/plumed/patches/gromacs-2024.3.diff/src/gromacs/mdrun/minimize.cpp.preplumed
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lib/plumed/patches/gromacs-2024.3.diff/src/gromacs/mdrun/replicaexchange.cpp
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lib/plumed/patches/gromacs-2024.3.diff/src/gromacs/mdrun/replicaexchange.cpp.preplumed
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lib/plumed/patches/gromacs-2024.3.diff/src/gromacs/mdrun/replicaexchange.h
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lib/plumed/patches/gromacs-2024.3.diff/src/gromacs/mdrun/replicaexchange.h.preplumed
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lib/plumed/patches/gromacs-2024.3.diff/src/gromacs/mdrun/rerun.cpp
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lib/plumed/patches/gromacs-2024.3.diff/src/gromacs/mdrun/rerun.cpp.preplumed
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lib/plumed/patches/gromacs-2024.3.diff/src/gromacs/mdrun/runner.cpp
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lib/plumed/patches/gromacs-2024.3.diff/src/gromacs/mdrun/runner.cpp.preplumed
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lib/plumed/patches/gromacs-2024.3.diff/src/gromacs/modularsimulator/expandedensembleelement.cpp
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lib/plumed/patches/gromacs-2024.3.diff/src/gromacs/modularsimulator/expandedensembleelement.cpp.preplumed
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lib/plumed/patches/gromacs-2024.3.diff/src/gromacs/taskassignment/decidegpuusage.cpp
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lib/plumed/patches/gromacs-2024.3.diff/src/gromacs/taskassignment/decidegpuusage.cpp.preplumed
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lib/plumed/patches/gromacs-2024.3.diff/src/gromacs/taskassignment/include/gromacs/taskassignment/decidegpuusage.h
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lib/plumed/patches/gromacs-2024.3.diff/src/gromacs/taskassignment/include/gromacs/taskassignment/decidegpuusage.h.preplumed
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lib/plumed/patches/gromacs-2025.0.config
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lib/plumed/vim/help/RMSD_VECTOR.txt
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lib/plumed/vim/help/SANS.txt
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lib/plumed/vim/help/SAXS.txt
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lib/plumed/vim/help/SECONDARY_STRUCTURE_RMSD.txt
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lib/plumed/vim/help/SELECT.txt
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lib/plumed/vim/help/SELECTOR.txt
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lib/plumed/vim/help/SELECT_COMPONENTS.txt
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lib/plumed/vim/help/SELECT_WITH_MASK.txt
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lib/plumed/vim/help/SHADOW.txt
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lib/plumed/vim/help/SORT.txt
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lib/plumed/vim/help/SORT_SCALAR.txt
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lib/plumed/vim/help/SORT_VECTOR.txt
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lib/plumed/vim/help/SPHERICAL_KDE.txt
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lib/plumed/vim/help/STATS.txt
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lib/plumed/vim/help/SUM.txt
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lib/plumed/vim/help/SUM_GRID.txt
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lib/plumed/vim/help/SUM_MATRIX.txt
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lib/plumed/vim/help/SUM_SCALAR.txt
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lib/plumed/vim/help/SUM_VECTOR.txt
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lib/plumed/vim/help/TEMPLATE.txt
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lib/plumed/vim/help/TIME.txt
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lib/plumed/vim/help/TORSION.txt
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lib/plumed/vim/help/TORSIONS.txt
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lib/plumed/vim/help/TORSION_SCALAR.txt
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lib/plumed/vim/help/TORSION_VECTOR.txt
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lib/plumed/vim/help/TRANSPOSE.txt
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lib/plumed/vim/help/UNITS.txt
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lib/plumed/vim/help/UPDATE_IF.txt
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lib/plumed/vim/help/UPPER_WALLS.txt
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lib/plumed/vim/help/UPPER_WALLS_SCALAR.txt
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lib/plumed/vim/help/UWALLS.txt
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lib/plumed/vim/help/VOLUME.txt
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lib/plumed/vim/help/VORONOI.txt
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lib/plumed/vim/help/VSTACK.txt
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lib/plumed/vim/help/WHOLEMOLECULES.txt
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lib/plumed/vim/help/WRAPAROUND.txt
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lib/plumed/vim/help/XANGLES.txt
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lib/plumed/vim/help/XDISTANCES.txt
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lib/plumed/vim/help/XYTORSIONS.txt
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lib/plumed/vim/help/XZTORSIONS.txt
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lib/plumed/vim/help/YANGLES.txt
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lib/plumed/vim/help/YDISTANCES.txt
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lib/plumed/vim/help/YXTORSIONS.txt
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lib/plumed/vim/help/YZTORSIONS.txt
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lib/plumed/vim/help/ZANGLES.txt
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lib/plumed/vim/help/ZDISTANCES.txt
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lib/plumed/vim/help/ZXTORSIONS.txt
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lib/plumed/vim/help/ZYTORSIONS.txt
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lib/plumed/vim/scripts.vim
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lib/plumed/vim/syntax/plumed.vim
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lib/plumed/vim/syntax/plumedf.vim
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libdata/pkgconfig/plumed.pc
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libdata/pkgconfig/plumedInternals.pc
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libdata/pkgconfig/plumedWrapper.pc
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share/bash-completion/completions/plumed
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