!IV.5. Dimethylphosphate-Sodium complex with freely moving sodium

!This input show how to allow tranlational/rotational degrees of freedom
!for molecules considered 'solute' by the program.

FILE dmpna
TITL Na+DMP-: Kollman-Straatsma(Na+)
TITL SPC water. H-R PBC
HRDW VC32          ! 32-bit vector algorithm
SVVC SPCC 7.75     ! Solvent spherical cutoff
SUVC MIGC 0.0
! MI on the solute based on group center distances
SUUC MIMC          ! Molec-based MI for intrasolute
PBCN RECT 32.031  21.354 21.354
! Rectangular PBC, long box
TEMP 298   |  NSLV 485
!Simulation at 298 Kelvin with 485 solvent molecules
STEP 0.1 0.0 0.55 40.0 10
! 0 slt stepsize, 0.55 Å, 40 deg solvent steps
SVPT TIP3 TIP3 ! Solvent-solvent pot: TIP3P
SUPT AM94      ! Solute-solvent pot: AMBER
SAMP FBSC 0.5  ! Scaled force-biased sampling
    2
 4.00   0.2   7.0     1.0
MOVE PRSP NRST
! Preferential sampling based on nearest slt atom dist
    3
 3.00   3.5   4.0    03.0    7.0    1.0

PMOD AM94 1    ! Potential library modification
   49   46
   11  1.59955E+00     0.478833E-01
! Solute's "own" solvent will be used for slt-slv
SLTA  SMPL MMC READ 8
! 8 solute atom - regular solute, read from input stream
   38     0.0       0.0       0.0       0.91200    1
   35     0.74000   0.0       1.28171  -0.65500    1
   35     0.74000   0.0      -1.28171  -0.65500    1
   37    -0.99164  -1.25560   0.00000  -0.41000    1
   37    -0.99164   1.25560   0.00000  -0.41000    1
    4    -1.92075   1.43300   1.07251   0.10900    1
    4    -1.92075  -1.43300  -1.07251   0.10900    1
   49     2.70000   0.0      -0.00000   1.00000    2
PARD UNIF SHCY 1.0 0.3 0.0 1.0 0.3 0.0 ~
1.0 0.3 0.0 1.0 -1 ! Last slt group is independently moved
DSTC NONE   ! No distribution function calc
SLFT BASC   ! Basic self tests performed
CNFG READ ASCI ! Input from dmpna.crd in ASCII
RUNS 2000000 50000 1000000 0100000 100000
! Run 2M steps
STOP

!Files needed for run:
!dmpna.crd: initial configuration.
!Files created by the run:

!    * dmpna.ckp: checkpoint file after the first run;
!    * dmpna.2.crd: final configuration after the run.