small updates and removing X permissions

applications/solvers/molecularDynamics/gnemdFoam/gnemdFoam.C

...lecularDynamics/mdEquilibrationFoam/mdEquilibrationFoam.C

...larDynamics/mdEquilibrationFoam/readmdEquilibrationDict.H

src/lagrangian/Allwmake

...elationFunction/bufferedAccumulator/bufferedAccumulator.C

...elationFunction/bufferedAccumulator/bufferedAccumulator.H

...lationFunction/bufferedAccumulator/bufferedAccumulatorI.H

...ationFunction/bufferedAccumulator/bufferedAccumulatorIO.C

...an/molecularDynamics/molecule/distribution/distribution.C

...an/molecularDynamics/molecule/distribution/distribution.H

...n/molecularDynamics/molecule/distribution/distributionI.H

.../molecularDynamics/molecule/distribution/distributionIO.C

...gian/molecularDynamics/molecule/mdTools/averageMDFields.H

...an/molecularDynamics/molecule/mdTools/calculateMDFields.H

...ngian/molecularDynamics/molecule/mdTools/createMDFields.H

src/lagrangian/molecularDynamics/molecule/mdTools/md.H

...larDynamics/molecule/mdTools/meanMomentumEnergyAndNMols.H

...angian/molecularDynamics/molecule/mdTools/resetMDFields.H

...lecularDynamics/molecule/mdTools/temperatureAndPressure.H

...namics/molecule/mdTools/temperatureAndPressureVariables.H