Force Field Xtest.RaoBlackwellEstimator(1)
Synopsis
test.RaoBlackwellEstimator [-hV] [--aFi=traj] [--bootstrapIter=100000] [--ch=<chain>] [--dS=<selection>] [--dsR=<selection>] [--numSnaps=-1] [--skip=-1] [--sR=<selection>] [--startSnap=-1] [--writeFrequency=100] files…
Description
Use the Rao-Blackwell estimator to get a free energy difference for residues in a CpHMD system.
Options
- --aFi, --arcFile=traj
- A file containing the the PDB from which to build the ExtendedSystem. There is currently no default.
- --bootstrapIter=100000
- Number of bootstrap iterations. Set -1 for no bootstrapping.
- --ch, --chain=<chain>
- Single character chain name (default is 'A').
- --dS, --discreteState=<selection>
- Specified residues are set to discrete state when doing analysis.
- --dsR, --discreteStateResidues=<selection>
- Specified residues are set to discrete state when doing analysis.
- -h, --help
- Print command help and exit.
- --numSnaps=-1
- Number of snapshots to use from an archive file. Default is all.
- --skip=-1
- Calculate energies on snaps with this interval.
- --sR, --specifiedResidues=<selection>
- Specified residues to do analysis.
- --startSnap=-1
- Start energy evaluations at a snap other than 2.
- -V, --version
- Print the Force Field X version and exit.
- --writeFrequency=100
- Calculate the RBE and print at this snapshot read frequency.