LIO plus MM software

Common

LIO is designed with QM/MM (electrostatic embedding) simulations as its main goal. As such, this page deals with LIO/MM compilations for three sofrware packages: AMBER, GROMACS and HYBRID. This is generally easy for all three cases. Since the AMBER installation needs only sander, you can just download AmberTools which is freely available.

In all cases, you must first have LIO already installed, and liohome.sh sourced (see the LIO installation page for more info).

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LIO-AMBER

The only difference with a regular AMBER installation is that the configure step must be done including the -lio option. For example:

./configure -lio gnu

LIO only works with sander, since pmemd does not have a QM/MM interface; nevertheless, the computational cost of QM/MM simulations usually lie on the QM-region treatment, therefore rendering the GPU acceleration for the MM code useless.

In the develop branch, certain features need an upgraded interface for LIO-AMBER. This interface (which is a single file) must be copied from LIOHOME/dat/ambermod/ to the sander source code folder before attempting an AMBER installation. This last folder is usually AMBERHOME/AmberTools/src/sander/.

LIO-HYBRID

HYBRID may be compiled with LIO by just adding the qm_lio option in HYBRID:

make qm_lio=1

LIO-GROMACS

The GROMACS interface is still experimental, and as such it is no readily available in the official GROMACS releases. As such, you must download our own GROMACS fork in order to attempt this installation. The only difference with a regular GROMACS installation is the addition of some options in the cmake step:

cmake ../gromacs_path/ -DGMX_QMMM_PROGRAM="lio“ -DLIO_LINK_FLAGS=“-lg2g –llio-g2g”