This script runs AMS in parallel
Export the namd executable path as namd !
I need two files and you have to pass me the path to FILE 2 by command line!
FILE 1: file with the standard namd variables
 - don't need to include the outputname variable
 - include colvar statements
 - do not include freqs for dcd and etc
 - do not include the temperature command
 - include a variable called temperature with the temperature value
 - if using periodic cell include the dimensions and center (even if you think it is unnecessary)
FILE 2: principal file (file passed in command line)
 - set the path for the namd file (FILE 1)
 - set the user parameters listed above:
	outdir = root directory to save all the ams instances directories
	numinst = number of AMS instances
	freenodes = number of nodes that can be occupied
	numrep = number of replicas for EACH instance
	amstype = single, mult or var
	zmin = minimum value for the reaction coordinate (only define if amstype == var)
	zmax = AMS_thresholdMaxZ
	timelimit = simulation time limit in hours
	icprefix = prefix for coor, vel and xsc files from initial condition
		   if amstype is mult the files have to be named prefix.n, were n=0,...,numrep-1
	zone = path to tcl script that returns -1 if in zone A, 1 if in zone B and 0 otherwise
	measure = path to script to calculate the reaction coordinate
	variables = path to tcl script that returns the internal colvars variables to print in the trajectory file
	coordinates = pdb file
	amssteptime = step time for ams
	tokill = minimal number of replicas to kill
	getpaths = on or off
	charmrunp = number of processors to use (if not given the command will be namd2 without charmrun)
	removefiles = yes or no
FILE toall_smart:
 - Change varibles smart_path (path to all the smart files) and amsscript (path to ams script to run).
 - Export the path to toall_smart.sh as toall_smart