# configuration for parallel string method simulations
######################################################

# job id (always start with 0 then increment by 1)
set job_id 0
# (default: 0)

# number of iterations; (required)
set runs 1000
# when restarting, note that the number of previous runs will be determined from the *restart.xsc files; whatever is performed already will be subtracted from "runs"

# number of copies per image; default: 1
set nc 1
# number of replicas must be a multiple of nc
# number of images is not specified directly but determined from the number of replicas divided by number of copies (nr = ni * nc; i.e., ni = nr/nc)

# number of samples per replica; default: 1
set ns 5
# number of samples generated per replica at every iteration
# ns can replace nc if there are not enough processors available
# ns and nc can also be combined for maximum efficiency

# simulation time for equilibration stage (restraining); default: 500
set runE 2500

# simulation time for drifting stage (releasing); default: 500
set runR 2500

# colvars config file (must have a harmonic block; the centers and force constant of this block are overriden by the info provided below)
set colvars_conf colvars.conf

# harmonic block used (must be defined in colvars); required
set harm "harm"

# force constatnt for the restraining stage; required
set force 10000

# all collective variables used (they all have to be in one harmonic block); required
set cvs { q1 q2 q3 q4 q5 q6 q7 q8 q9 q10 q11 q12 }

# dimension of collective variables; default: 1
#set cvsd { 4 4 4 4 4 4 4 4 4 4 4 4 }
set cvsd 4
# note: if only one number provided all cvs will have that dimension

# metric used for the distance calculations (each number provides a weight for each cv in distance calculation; i.e., the given numbers are the components of a diagonal matrix that represents an isotropic metric tensor); default: 1
#set cvsm { 1 1 1 1 1 1 1 1 1 1 1 1 }
set cvsm 1
# note: if only one number provided all cvs will have that weight

# initial reparametrization (if 1; it will reparametrize/smoothen at the beginning, otherwise will use the average); default: 0
set initial_reparam 1

# smoothing parameter; default: 0
set smooth 1
# ranges between 0 and the number of images; recommended value is 1 (0 skips smoothing)

######################################################
# set the output directories here (required):
set output_root "output/%s/glpt"
# if **/%s/** is used, all copies of the same image will be put in the same directory (the directories should be already made)
# otherwise, all output files will be put in the same directory.

######################################################
# the following is only relevant when job_id = 0;
set input_root "input/init.%s" ; # initial conformations; required for job_id=0
set usevel 0 ; #do you have *.vel files? (0 or 1); default: 0
set temperature 310; #specify the temperature if usevel is set to 0
set usexsc 1 ; #do you have *.xsc files? (0 or 1); default: 0
#set cellinfo { {130 0 0} {0 130 0} {0 0 200} {0 0 0} } ; cellBasicVectors 1 to 3 and cellOrigin (not needed if usexsc is set to 1)

######################################################
set system_conf ../../system/glpt.inp
# this is your usual namd config file without the following commands:
# outputname, bincoordinates, binvelocities, extendedsystem, firsttimestep, and run as well as colvars related commands

######################################################
# generic configuration file for string method with swarms of trajectories:
source ../../codes/smwst.namd