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# interface to beus.namd (bias-exchange umbrella sampling script)
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# mpirun 
# running on most supercomuters available with namd runscript:
# ./run <configfile> <logfile> <total_num_nodes> +replicas <num_replicas> +stdout <logfile>.%d
# <total_num_nodes> must be a multiple of <num_replicas>
# example: ./runbatch_cuda job0.conf job0.log 100 +replicas 100 +stdout output/job0.log.%d

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

set colvars_conf input.in

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

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# the following is only relevant when job_id = 0;
set input_root "input/Win_%s" ; # initial conformations; required for job_id=0 (%s represents replica_id)
set usevel 1 ; #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)

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set system_conf OMPF.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

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# generic configuration file for bias-exchange umbrella sampling:
source base_job0.tcl