!IV.8. Creation/annihilation polynomial path thermodynamic integration

!This is an example of a different free energy simulation
!type: calculation the solvation excess Helmholtz free
!energy of NO in water with polynomial thermodynamic integration over a
!creation/annihilation path.

FILE NO_ti 10
TITL Excess Helmholtz free energy of solvation of NO in water
TITL Calculated by three-point Gaussian quadrature
PRNT ECHO 
HRDW VC32          ! 32-bit vector
SVVC MINI         ! Solvent cutoff
SUVC MIGC 0.0      ! MI on the solute
PBCN RECT 14.74    !Rectangular PBC
MOVE RAND          ! Random selections
!Set creation/annihilation TI using the first quadrature point
!Lambda exponents: 4, 3, 2 (for 1/r^12, 1/r^6, 1/r terms, resp.)
FREE TICA  NOMX
 4.0   3.0  2.0     0.112702
TEMP 298
NSLV 108
STEP  0.00   00.0   0.40    35.0 50
SVPT TIP3 TIP3 ! Solvent-solvent potential is TIP3P
SUPT CHRM
!Add NO parameters
PMOD CHRM 2
  150   70    3.3    N/NO
    7 1.824            0.17
  151   70    3.3    O/NO
    8 1.751            0.159
SAMP METC 0.5
!Make sure the dummy atoms in the first copy are treated as one molecule
MOLD 2 2 4
!Solute has 4 atoms, 4 free energy atoms, and the first copy has 2 atoms
SLTA  SMPL MMC READ 4 4 2    !Dummy solute
 DUM      -.570      000.0    0.00000   0.00000    1
 DUM      0.58       000.0    0.00000   0.00000    1
  150     0.57000    000.0    0.00000   0.02800    2
  151     -.58000    000.0    0.00000  -0.02800    2
DSTC NONE
CNFG READ ASCI NOFX
FIXD FIXD 2500000
!Equilibration
RUNS 2000000  100000  100000 500000  100000
RMCK !Remove unneded checkpoint file
!Production run, runnumber=11
RUNS 10000000  100000  100000 500000  100000
FILE  NO_ti  20
!Set lambda to the 2nd quadrature points
FREE TICA  NOMX
 4.0   3.0  2.0     0.500000
CNFG READ ASCI NOFX  12
RUNS 2000000  100000  100000 500000  100000
RMCK !Remove unneded checkpoint file
!Production run, runnumber=21
RUNS 10000000  100000  100000 500000  100000
FILE  NO_ti  30
!Set lambda to the 3rd quadrature points
FREE TICA  NOMX
 4.0   3.0  2.0     0.887298
CNFG READ ASCI NOFX  22
RUNS 2000000  100000  100000 500000  100000
RMCK !Remove unneded checkpoint file
!Production run, runnumber=31
RUNS 10000000  100000  100000 500000  100000
!Evaluate the quadrature from the data on the three checkpoint files
TIQU REGL ALL 3 11 10
    0  001    0
STOP SLFT

!Files needed for run:

!    * NO_ti.10.crd: initial configuration.

!Files created by the run:

!    * NO_ti.11.crd: configuration after equilibration
!    * NO_ti.11.ckp: checkpoint file with the data for the 1st quadrature
!      point
!    * NO_ti.12.crd: configuration after 1st quadrature run
!    * NO_ti.21.crd: configuration after equilibration
!    * NO_ti.22.crd: configuration after 2nd quadrature run
!    * NO_ti.21.ckp: checkpoint file with the data for the 2nd quadrature
!      point
!    * NO_ti.31.crd: configuration after equilibration
!    * NO_ti.32.crd: configuration after 3rd quadrature run
!    * NO_ti.31.ckp: checkpoint file with the data for the 3rd quadrature
!      point