set frameid 128
set neighborid 0
#**********************************************************
#  Name production
#  Date 2014-12-12
#  * Generated with Automatic NAMD input file generator by Lane Votapka
#**********************************************************

set inpname	../ens_equil/ens_equil_0_1
set outname	forward$frameid
firsttimestep	0

# input

amber                   yes
parmfile                ../building/holo.prmtop

readexclusions          yes

coordinates             ../reverse/pos${neighborid}_${frameid}.pdb  ;# the starting positions of all atoms in the system; sampled from the equilibrium simulations
Velocities              ../reverse/vel${neighborid}_${frameid}.pdb  ;# the starting velocities of all atoms in the system; sampled from the equilibrium simulations or generated using a Maxwell-Boltzmann distribution

ExtendedSystem          $inpname.restart.xsc


# force field parameters
exclude                 scaled1-4
1-4scaling              1.0
cutoff                  14

switching               on
switchdist              12
pairlistdist            16
margin			0.0
rigidBonds		all
rigidTolerance		0.0005

# integrator params
timestep                1.0
useSettle               on

PME                     yes



PMEGridSpacing          1.0

nonbondedFreq           2
FullElectFrequency      2
stepspercycle           20


useGroupPressure        no
useFlexibleCell         no
useConstantArea         no

#PBC




wrapWater               on
wrapAll			off
wrapNearest		on
xstFile                 $outname.xst
xstFreq                 1000


### TCL script section
tclforces               on ;# this command allows the milestoning.tcl script to be referenced at every timestep
tclforcesscript         ../../../milestoning.tcl ;# the path to the milestoning script


# output


outputname              $outname
dcdfile                 $outname.dcd
restartname             $outname.restart
restartfreq             1000
dcdfreq                 1000
binaryoutput            yes



outputEnergies          1000





numsteps                100000



# tclforces variables
  set ID 1 ;# the ID of this trajectory

  set SCRIPT_INTERVAL 5 ;# number of timesteps before script should be evaluated. Examples: 1=script evaluated every timestep. 5=script eval'd every 5th timestep, ...
  set LIGROT False ;# whether we care about ligand rotation
  set RECROT False ;# whether we care about receptor rotation
  set ABORT_ON_CROSSING False
  set PHASE forward ;# can be 'forward' or 'reverse'
  set CARE_ABOUT_SELF False ;# whether we care about the milestone's self in this simulation
  set whoami 1 ;# the index of the current
  set whoami_rot 6
  set MAIN_NEIGHBOR {N o n e}
  set GRID_EDGE_RAD 0.0 ;# radius to the edge of the grid from the center
  set LIGRANGE {1} ;# the indeces of the atoms that define the ligand
  set RECRANGE {2} ;# the indeces of the atoms that define the receptor
  set RECPA1_LIST {} ;# the list of relatively immobile atoms that define the receptor's 1st PA
  set RECPA3_LIST {} ;# the list of relatively immobile atoms that define the receptor's 3rd PA
  set FHPD_FILE ../reverse/fhpd.txt ;# the location of the file where we will write FHPD trajectory ID's
  set MILESTONE_LIST {
{ id 0 siteid site1 shape sphere center_type coord absolute True radius 6.000000 center { 0.000000 0.000000 0.000000 } side outside end True }
{ id 1 siteid site1 shape sphere center_type coord absolute True radius 7.000000 center { 0.000000 0.000000 0.000000 } side outside end False }
{ id 2 siteid site1 shape sphere center_type coord absolute True radius 8.000000 center { 0.000000 0.000000 0.000000 } side outside end False }
{ id 3 siteid site1 shape sphere center_type coord absolute True radius 9.000000 center { 0.000000 0.000000 0.000000 } side outside end False }
{ id 4 siteid site1 shape sphere center_type coord absolute True radius 10.000000 center { 0.000000 0.000000 0.000000 } side outside end False }
{ id 5 siteid site1 shape sphere center_type coord absolute True radius 11.000000 center { 0.000000 0.000000 0.000000 } side outside end True }
{ id 6 siteid site1 shape rotational absolute False quaternion {1 0 0 0} adj_quat_list {{ }} adj_side_list { unk unk } side uncrossed end False }
};# a list of milestones to be converted to arrays
  set SITEID site1 ;# the ID if the current site
  set MAX_NUM_STEPS 0 ;# the maximum number of steps before starting a new crossing phase