# configuration for replica exchange scripts

# run simulation: 
#   mkdir output
#   (cd output; mkdir 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15)
#   mpirun -np 16 -hostfile hostfile $bindir/namd2 +replicas 16 job0.conf +stdout output/%d/job0.%d.log
# the number of MPI ranks (-np) must be a multiple of the number of replicas (+replicas)

# to continue:
#   mpirun -np 16 -hostfile hostfile $bindir/namd2 +replicas 16 job1.conf +stdout output/%d/job1.%d.log
# increase num_runs below if job completed, or use latest restartXXX.tcl file available
# be sure to increment jobX for +stdout option on command line

# view in VMD:  source job0.conf; source ../show_replicas.vmd
# add continued:   source job1.conf; source ../show_replicas.vmd
# show both:  vmd -e load_all.vmd

# sort into single-temperature trajectories:
#   $bindir/sortreplicas output/%s/stretch_alanin.job0 16 10
#   $bindir/sortreplicas output/%s/stretch_alanin.job1 16 10

set num_replicas 16
set temperature 300
set steps_per_run 1000
set num_runs 10000
# num_runs should be divisible by runs_per_frame * frames_per_restart
set runs_per_frame 10
set frames_per_restart 10
set namd_config_file "alanin_base.namd"
set output_root "output/%s/stretch_alanin" ; # directories must exist
set input_root "input/alanin.initial.%d" ; # initial configurations

# this function returns the center of a biasing potential
proc replica_bias { i } {
  return [list lenpot "centers [expr 17 + $i]"]
}

# this function returns a list of the neighbors of a replica
proc replica_neighbors { i } {
  global num_replicas
  if { $i % 2 } { set s -1 } { set s 1 }
  set result {}
  foreach { d } { $s -$s } {
    set j [expr $i + $d]
    if { $j < 0 || $j >= $num_replicas } {
      lappend result $i ; # swap with self
    } {
      lappend result $j
    }
  }
  return $result
}

# the following used only by show_replicas.vmd
set psf_file "alanin.psf"
set initial_pdb_file "alanin.pdb"
set fit_pdb_file "alanin.pdb"