!IV.11. Proximity analysis, trajectory filtering

!This input show how to set up proximity analysis of a trajectory given
!as a series of PDB files and how to use this analysis to filter this
!trajectory file.

FILE 5ht1
TITL GCE run with fixed solute
HRDW VC32        ! 32-bit vector
SVVC SPCC 7.75  ! Solvent-solvent cutoff
SUVC MIGC 0.0 ! Group-cent based MI on the slt
PBCN RECT 70.0 75.0 58.0  !Rectangular PBC
TEMP 298
SVPT TIP3 TIP3
SUPT CHRM  ! Solute-solvent potential is CHARMM
MOLD 1 3192
SLTA SMPL MMC FILE  3192
!Solute description is read from 5ht1.slt in MMC format
TRAJ ALLP RGFX ALST !Open trajectory in PDB format
FILT SOLV TRAJ ALLP SHL1 RVDW 1.4 0 0 10
!filter out solvents outside the first shell
TRAJ ALLP RGFX ALST 0 1 11
!Open filtered trajectory
PXCR WDEN BISE
!select proximity criterion type
PXWR ASCI
!Create ASCII proximity information file
PXBE -100.0  2.0
!Calculate solute-solvent energy analysis
SCAN TRAJ 250000 1 5000 0 2000 1000 2  3 1
!Run analysis
FILE 5ht1 1    !Reset run number to one
TRAJ ALLP RGFX ALST 0 1 11 !Open filtered traj
FILT ENRG TRAJ ALLP  -100.0 -1.0 10
!Filter solvent by the solute-solvent energy
TRAJ ALLP RGFX ALST 0 1 11
!Open filtered trajectory again
FILT ENRG TRAJ ALLP  -1.0 100.0 11
!Filter solvent by solute-solvent energy using a different range
TRAJ ALLP RGFX ALST 0  1 21
!Open trajectory after 1st energy filter
PXWR OFF  ! turn of pxi file since it is incompatible with
!the filtered trajectories
DENF INSG 0 1 0
!Create single configuration aggregating all solvents
TRAJ ALLP RGFX ALST 0 1 22
!Open trajectory after 2nd energy filter
DENF INSG 0 1 0
!Create single configuration aggregating all solvents
STOP

!Files needed for run:

!    * 5ht1.hst: Trajectory file in PDB format

!Files created by the run:

!    * 5ht1_11.hst: Filtered (1st shell only) trajectory file
!    * 5ht1.pxi: proximity information file (see PXWR )
!    * 5ht1.ckp: checkpoint file
!    * 5ht1.pxc: proximity analysis checkpoint file
!    * 5ht1_21.hst: Filtered (1st energy filtering) trajectory file
!    * 5ht1_22.hst: Filtered (2nd energy filtering) trajectory file
!    * 5ht1_den_21.dat: Aggregated solvents (in Insight free format) file
!      from 1st energy filtering
!    * 5ht1_2.dat: Aggregated solvents (in Insight free format) file from
!      2nd energy filtering