COSMO and COSMO-RS calculation with Turbomole and COSMOTherm

The documentation is found in the Turbomole manual on page 108.

The method is available for SCF, DFT, and RI-DFT calculations.
Both energies and gradients can be calculated.
No symmetry is allowed (C1).

  1. Set up a normal calculation with define

  2. Run comsoprep
    Typically, you change only epsilon (the dielectric constant)
    If there are no hydrogens in the structure, you have to set rsolv also. Set it to the radius of the smallest atom in the molecule (H = 1.30 ┼ (default), O = 1.72 ┼, N = 1.83 ┼, C = 2.00 ┼, S = 2.16 ┼).
    In the radius definition menu, enter
    r all o
    (Note that the radii given are in atomic units, whereas they are written in the control file in ┼ngstr÷m).

  3. Now you can run a energy calculation or a geometry optimisation in the normal way
    dscf >logfil
    jobex -c 200 -ri


Ulf, 3/10-00


CosmoTherm

So far, the program is only installed on Platon and on my Mac (installation failed on gefion)
The program is in /lunarc/nobackup/projects/bio/COSMO/COSMOthermX13
The binaries are
/lunarc/nobackup/projects/bio/COSMO/COSMOthermX13/COSMOtherm/BIN-LINUX/cosmotherm
/lunarc/nobackup/projects/bio/COSMO/COSMOthermX13/COSMOthermX/COSMOthermX13

You should set in your profile
export COSMOTHERM_HOME=/lunarc/nobackup/projects/bio/COSMO/COSMOthermX13/COSMOtherm/CTDATA-FILES

The program is run by
cosmotherm in.inp

The program requires that the input file has the extension *.inp.
The output is in the file with the same starting and the extension *.out



Solvation calculation with COSMO-RS

Recommended level of theory BP/TZVP (NB not def2-)
  1. Optimise the geometry in solvent with a specific (finite) dielectric constant
  2. Run a single-point energy calculation with eps=infinite. Keep the out.ccf file.
  3. Optimise the geometry also in vacuum in a separate directory.
  4. Run turdenergy in this directory to get the out.energy file
  5. Move the out.energy to the directory with the eps=infinite calculation.
  6. Run COSMOTherm in this directory with the following input:

    ctd=BP_TZVP_C30_1301.ctd
    EHFile
    Title
    f=h2o_c0  fdir=/lunarc/nobackup/projects/bio/COSMO/COSMOthermX13/COSMOtherm/DATABASE-COSMO/BP-TZVP-COSMO
    f=out.ccf fdir=.
    tc=25 Henry=1 GSOLV

    ctd is the name of the parameter file
    cdir is the directory of the parameter files
    fdir is directory of the input files, first (line 4) the data-base file and then (line 5) the current directory. Note that fdir must come on the same line as f=...
    ldir is the directory where the licence file is found
    AUTOC use all ccf files in the current (fdir) directory as different conformations
    WCMN write the compound/mixture name to the right (to allow for grepping out results)
    EHfile find the gas phase energy in Hargree in current directory in the name out.energy. This file should only contain the energy, nothing else.
    The first f specifies the solvent. It needs to have the proper COSMO name, found in /lunarc/nobackup/projects/bio/COSMO/COSMOthermX13/COSMOtherm/DATABASE-COSMO/BP-TZVP-COSMO.csv
    The second f specifies the solute
    ef specifies the name of the energy file
    tc specifies the temperature in C.
    Henry=1 asks the program to calculate the Henry coefficients for compound 1. It is necessary.
    GSOLV asks the program to calculate the free energy of solvation.

  7. There are two lines of Gibbs free energy of solvation are given in the *.out file.
    The first is for a molecule of the solvent in the solvent.
    The second is for your compound in the solvent (the one you want).
    grep 'Gibbs Free Energy of Solvation' *out
If you have a large charge of the molecule, you may need to use the undocumented option ADEG, put on the same line as EHFile. Otherwise, you get:
     WARNING: Energy difference E_COSMO-E_GAS of molecule    2 is unreasonably large: E_COSMO-E_GAS =  1.6050433344E+03kcal/mol
  WARNING: Using E_COSMO-E_GAS =  3.0000000000E+02kcal/mol instead



Remove COSMO-related keywords from control

kdg cosmo
kdg cosmo_atoms
kdg cosmo_out
kdg cosmo_correlated

These commands can now be run by command
rmcosmo

Change to an infinite dielectric constant

grep -v 'epsilon=' control >tmp.control
diff control tmp.control
\mv tmp.control control



Automatically run cosmoprep for eps=4

cosmoprep <<EOF
4








r all o
r "fe" 2
r "ni" 2
r "mg" 2
*

EOF


If the $COSMOTHERM_HOME variable is not properly set, you need to start with:
ctd=BP_TZVP_C30_1301.ctd cdir=/lunarc/nobackup/projects/bio/COSMO/COSMOthermX13/COSMOtherm/CTDATA-FILES fdir=/lunarc/nobackup/projects/bio/COSMO/COSMOthermX13/COSMOtherm/DATABASE-COSMO/BP-TZVP-COSMO ldir=/lunarc/nobackup/projects/bio/COSMO/COSMOthermX13
EHFile
Title
f = h2o_c0
f=out.ccf fdir=.
tc=25 Henry=1 GSOLV