!IV.13. Generic site calculation

FILE GENSfile
SVVC SPCC 10.0  ! Solvent cutoff
SUVC MIGC 0.0   ! MI on the solute
PBCN RECT 56.0011  67.5172  81.0524 !Rectangular PBC 
SVPT TIP3 TIP3
SUPT CHRM
SLTA SMPL MMC FILE 5402  0 0 0 1
CNFG READ ASCI
TRAJ ALLH FLEX ALST
GENS CALC FIXI GETH SPDB FSRT ~
 125 5000000 1 10000 6.5 0.01 0.10 6.0 0.2 100 10 
!Number of sites requested (initially): 125
!Number of simulation steps to read: 5000000
!Use every 1-th config (counted in MC stepnumbers)
!Discard the first 10000 MC steps
!For the matching, consider only sites within 6.5 Å
!Convergence threshold for the Hungarian method matching: 0.01
!Convergence threshold for the RMSD between iterations: 0.1 
!Add a new site if a match is farther than 6.0 Å
!Previous site estimate will be mixed in with a factor of 0.2
!Maximum number of iterations over the trajectory: 199
!Minimum number of solvents in a configuration to be of use: 10
STOP NOSF

!Files needed for run:

!    * GENSfile.slt: Solute portion of the CHARMM CRD file
!    * GENSfile.CRD: Full configuration (including the solute) in CHARMM
!      CRD format
!    * GENSfile.hst: Simulation trajectory in CHARMM CRD format

!Files created by the run:

!    * GENSfile_gs.pdb: Solute plus the generic sites in PDB format
!    * GENSfile_gs_cmp.pdb: Solute plus a composite of solvents that are
!      nearest to sites, in PDB format
!    * GENSfile_gs_cmp.rep: Solute plus a the most representative
!      configuration from the simulation history, in PDB format