# configuration for replica exchange scripts

# run simulation: 
#   ../make_output_dirs.sh output 64
#   mpirun -np 64 -hostfile hostfile $bindir/namd2 +replicas 64 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 64 -hostfile hostfile $bindir/namd2 +replicas 64 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 64 10
#   $bindir/sortreplicas output/%s/stretch_alanin.job1 64 10

set num_replicas 19
set temperature 310
set steps_per_run 1000
set num_runs 500
# num_runs should be divisible by runs_per_frame * frames_per_restart
set runs_per_frame 10
set frames_per_restart 5
set namd_config_file "AmtB_base.conf"
set output_root "output/%s/AmtB-A" ; # directories must exist
set pdbRoot "input/start.%d.pdb"

proc replica_bias { i } {
  set c [expr 5.0 - $i]
  return [list Z "centers $c"]
}

proc replica_neighbors { i } {
  set n 19
  if { $i % 2 } { set s -1 } { set s 1 }
  set result {}
  foreach dx { $s 0 -$s } {
    set j [expr $i + $dx]
    if { $j < 0 || $j >= $n } {
      lappend result $i ;# swap with self
    } {
      lappend result $j ;# swap with neighbor
    }
  }
  return $result
}


# the following used only by show_replicas.vmd
set psf_file "input/AmtB-system.psf"
set initial_pdb_file "input/start.0.pdb"
set fit_pdb_file "input/start.0.pdb"