Using PLUMED

PLUMED functionality is enabled by using gmx mdrun -plumed plumed.dat.

The interface will look for an environment variable PLUMED_KERNEL that should contain the path and the name of a shared object that contains the PLUMED kernel, and usually is called libPlumedKernel.so.

If the library is not present an error message will inform the user to export the PLUMED_KERNEL variable.

Usually the PLUMED kernel is stored in $plumed_prefix/lib/libPlumedKernel.so, so it should be enough to export PLUMED_KERNEL=$plumed_prefix/lib/libPlumedKernel.so, where $plumed_prefix is the PLUMED installation prefix.

Configuration files for input

PLUMED input files are plain text files describing the analysis process and how PLUMED should influence the GROMACS simulation. The full documentation is available here

Limitations

The current implementation of the PLUMED interface does not support the following features:

  • interaction with GROMACS energy

  • PLUMED is incompatible with thread-MPI (PLUMED exits with an error when more than 1 thread-MPI rank is used)

  • The various replica exchange flavors are not yet implemented