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sampler.example.cfg
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[system]
active = if this system is currently being run (True/False)
jobname = prefix for slurm jobs
rootdir = root directory with other folders in it
scriptdir = /scratch/PI/rondror/rbetz/adaptivesampling/
featurized = path to featurized file with %d substituted for generation number
ligands = comma separated list of ligand resnames
num_ligands = number of ligands in the system
reference = Path to pre-stripped prmtop for alignment. psf also works.
refsel = Atom selection for stripped prmtops vs each other
canonical_sel = Atom selection for psf files
topologypsf = <deprecated>
prmtop = <deprecated>
[dabble]
dimensions = comma separated size of system (x,x,x)
forcefield = which forcefield to use (charmm/amber)
parameters = comma separated parameter files for dabble
topologies = comma separated topology files for dabble
minligdist = minimum separation between ligands (10.0 A)
minprotdist = minimum separation between ligand and protein (2.5 A)
solvent = solvent to use. Say either TIP3 or DEFAULT (for membrane)
excludesel = <deprecated>
[model]
num_clusters = number of initial clusters (300)
num_tics = number of tica components to retain (15)
tica_lag = lag in frames for tica (5 = 1 ns)
msm_lag = lag in frames for msm (50 = 10 ns)
macrostates = number of macrostates for final msm (50)
samplers = number of samplers to create each generation
extracellular_only = bool, scale features so extracellular only
sampleregion = atomselection string for valid region for resampling, for known binding site
criteria = resampling criteria to use. Either "hub_scores" or "populations" or "counts" supported
include_equilibration = whether or not to include equilibrated trajectories. True by default.
jobid = <deprecated>
[production]
generation = generation number we're on (start at 1, auto updates)
max_generation = stop running after this generation has been MSM'd
runlength = number of ns to run each simulation (100)
runpercent = percentage of runs that must reach minimum to do next generation range 0->1 (.9)
queue = queue to submit jobs to (rondror/rondror_high/owners)
submissions = minimum number of production jobs to keep in queue (5)
pressure = semiisotropic/isotropic/anisotropic (semiisotropic)
hmr = boolean if HMR should be used. Defaults to TRUE
extra_options = extra lines in the production mdin file go here (\n delimited). Good for aMD.
replicates = <deprecated>
productionids = <deprecated>