1) module module load icc_15.0.3-impi_5.0.3 2) unpack plumed 3) configure plumed ./configure --prefix=$INST 4) install make install 5) plumed environment export PATH=$PATH:/gscratch/pfaendtner/codes/plumed2-BayesBias/bin/bin export INCLUDE=$INCLUDE:/gscratch/pfaendtner/codes/plumed2-BayesBias/bin/include export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/gscratch/pfaendtner/codes/plumed2-BayesBias/bin/lib 6) which versions of GMX is BayesBias tree v 2.2 compatible with? -bash-4.1$ plumed patch -p warning:regcache incompatible with malloc PLUMED patching tool 1) amber14 4) gromacs-5.0.4 7) namd-2.8 2) gromacs-4.5.7 5) gromacs-5.1.2 8) namd-2.9 3) gromacs-4.6.7 6) lammps-6Apr13 9) qespresso-5.0.2 lets gry GMX 5.1.2. , maybe we will get lucky 7) unpack 5.1.2 8) run patch in the root directory -bash-4.1$ cd ../gromacs-5.1.2 -bash-4.1$ plumed patch -p warning:regcache incompatible with malloc PLUMED patching tool 1) amber14 4) gromacs-5.0.4 7) namd-2.8 2) gromacs-4.5.7 5) gromacs-5.1.2 8) namd-2.9 3) gromacs-4.6.7 6) lammps-6Apr13 9) qespresso-5.0.2 Choose the best matching code/version:5 MD engine: gromacs-5.1.2 PLUMED location: /gscratch/pfaendtner/codes/plumed2-BayesBias/bin/lib/plumed diff file: /gscratch/pfaendtner/codes/plumed2-BayesBias/bin/lib/plumed/patches/gromacs-5.1.2.diff sourcing config file: /gscratch/pfaendtner/codes/plumed2-BayesBias/bin/lib/plumed/patches/gromacs-5.1.2.config Linking Plumed.h and Plumed.inc (shared mode) Patching with on-the-fly diff from stored originals patching file ./src/gromacs/CMakeLists.txt patching file ./src/gromacs/mdlib/force.cpp patching file ./src/gromacs/mdlib/minimize.cpp patching file ./src/programs/mdrun/md.cpp patching file ./src/programs/mdrun/mdrun.cpp patching file ./src/programs/mdrun/repl_ex.cpp PLUMED is compiled with MPI support so you can configure gromacs-5.1.2 with MPI 9) plumed is patched, now try cmake and see if it works mkdir bin build_gromacs cd bin export GMXINST=`pwd` cd ../build_gromacs/ cmake .. -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=$GMXINST NOTE: to add different versions (like hte 8core version) : cmake .. -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=$GMXINST -DGMX_DEFAULT_SUFFIX=OFF -DGMX_BINARY_SUFFIX=_8c -DGMX_LIBS_SUFFIX=_8c 10) cmake was successful - next build and install make -j12 install 11) to use GMX 5.1.2 + PLUMED 2.2-BayesBias tree set these variables in your PBS file: module load icc_15.0.3-impi_5.0.3 export PATH=$PATH:/gscratch/pfaendtner/codes/plumed2-BayesBias/bin/bin export INCLUDE=$INCLUDE:/gscratch/pfaendtner/codes/plumed2-BayesBias/bin/include export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/gscratch/pfaendtner/codes/plumed2-BayesBias/bin/lib source /gscratch/pfaendtner/codes/gromacs-5.1.2/inst/bin/GMXRC 12) things have changed if you are familiar only with the old version that had all the individual gromacs commands, now you will use "gmx_mpi grompp" instead of "grompp" gmx_mpi grompp -c start.gro -p topol.top -f nvt.mdp to run a 4 replica multiple walkers job: mpiexec.hydra -np 8 gmx_mpi mdrun -plumed plumed.dat -multi 4 example = /gscratch/pfaendtner/codes/gromacs-5.1.2/multiple_walkers_test