!IV.7. Potential of mean force between dimethyl phosphate and sodium ions
!with adaptive umbrella sampling Mezei_87
!This input performs one type of free energy simulation Mezei_86_NYAS:
!it calculates the potential of mean force between two solute molecules
!using adaptive umbrella sampling.
FILE dmpna_pmf ! SPC water. H-R PBC
TITL Na+DMP-: Kollman-Straatsma(Na+),
TITL #1 4 Å range MI/RC G/A Run A
HRDW VC32 ! 32-bit vector hardware
SVVC SPCC 7.75 ! Solvent-solvent cutoff
SUVC MIGC 0.0 ! MI on the solute
PBCN RECT 32.031 21.354 21.354 !Rectangular PBC
MOVE SHCY ! Shuffled-cyclic selections
TEMP 298 | NSLV 485
STEP 0.10 0.0 0.55 40.0 10
! 0.1 Åslt stepsize, no slt rotation, 0.55 Å,
!40 deg solvent steps; solute moves at every 10th MC step
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
FREE PMF1 WRMM GEOC AUSE 2
!2-part PMF both parts of the slt moves
0.00 0.25 0.050 100.0 0.1
2 0 3 1 0.01 17. 0.0 0.0 0.00002 0.9
4 5 5 05 2.43 0.75
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 24 24 8
!3*8 solute atom - regular solute, last 1 atom is in the 2nd part
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
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 6.70000 0.0 -0.00000 1.00000 2
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
DSTC NONE
CNFG READ ASCI NOFX
! input from dmpna_pmf.crd in ASCII
RUNS 5000000 20000 2500000 0 100000 200000
STOP
!Files needed for run:
!dmpna_pmf.crd: initial configuration.
!Files created by the run:
! * dmpna_pmf.ckp: checkpoint file after the first run;
! * dmpna_pmf.2.crd: final configuration after the run.