!IV.12. Conformation filtering

!This example shows the elimination of waters that are not internal to
!the solute according to their circular variance. The filtering is done
!on a CHARMM CRD file.

FILE scednas
PRNT ECHO
SVVC SPCC 12.00 
SUVC SPGC 20.0 
PBCN RECT 99.00  99.00  99.00 ! Large box
NSLV 16426 
SVPT TIP3 TIP3 ! Solvent-solvent potential is TIP3
SUPT ATNO ! No potential information 
BRKB   32 ~
    92    97    92    99   231   236   231   238   292   297   292   299 ~
   323   328   323   330   404   409   404   411   593  3691   856   861 ~
   856   863  1149  1154  1149  1156  1784  1789  1784  1791  1825  1830 ~
  1825  1832  1882  2138  2030  2035  2030  2037  2090  2095  2090  2097 ~
  2299  2304  2299  2306  2318  2323  2318  2325  2467  2472  2467  2474 ~
  2792  2797  2792  2799
!Break spurious bonds that would confuse the routine establishing
!the molecular connectivities 
!Alternative: MOLD 1 3697
SLTA SMPL CRD FILE 3697
CNFG READ CHRM NOFX
FILT SOLV CONF CHRM CRCV RSIG 6.0 0.5 11
CNFG READ CHRM NOFX
FILT SOLV CONF CHRM CRCV RSIG 6.0 0.4 12
STOP

!Files needed for run:

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

!Files created by the run:

!    * scednas_11.CRD: Filtered conformation (keeping only internal waters)
!    * scednas_12.CRD: Filtered conformation (keeping only internal
!      waters), weakened filtering (keeping more waters)