Running LIO

LIO as a standalone.

In order to run LIO as a standalone, at least two files are needed:

• One containing atomic coordinates in XYZ format, for example:

3  
Water Molecule    
 8   71.762448    35.512769     96.172805   
 1   70.885172    36.746272     95.119946   
 1   73.544272    35.969662     96.043066

• One containing the input options in an &lio namelist, for example:

&lio
  natom       = 3
  open        = f
  charge      = 0
  nunp        = 0
  writeforces = t
  mulliken    = t
  dipole      = t
  fukui       = t
&end

Please be aware that the XYZ file should contain atomic numbers (8,1,6) and not atom names (O,H,C). Then, after sourcing liohome.sh ($ source /LIODIR/liohome.sh), LIO can be used via liosolo program:

$ liosolo -i inputfile.in -c crdfile.xyz

LIO with AMBER.

Please refer to the AMBER manual on how to perform QM/MM calculations. The only difference with routine calculations is that the input qm_method should be set to 'EXTERN' when running AMBER/LIO, and that and "&lio" empty namelist should be added in the AMBER input file. In order to edit LIO options, a separate file containing another &lio namelist must be created, and must named 'lio.in'. For an example of the &lio namelist, please refer to the section above.

IMPORTANT: Options set in the 'lio.in' file override those passed by AMBER, such as total charge or number of atoms.

LIO with GROMACS/HYBRID.

Please refer to either software's manual on how to run QM/MM calculations. There are no special input variables for LIO, but LIO options are kept in a separate 'lio.in' file as explained above.