Force Field XEnergy(1)
Synopsis
Energy [-ghmvV] [--in] [--pb] [--rg] [--aa=<selection>] [--ac=<selection>] [--ac2=<selection>] [--acRes=<selection>] [--acRes2=<selection>] [--dc=0. _ 0_] [--ec=0.0] [--fl=0] [--ia=<selection>] [-l=-1] [--np=1] [--pd=<dihedralAtoms>] [--sf=1.0] [--uaA=-1] [--uaB=-1] [--uc=<selection>] [--uc2=<selection>] file…
Options
- --dc, --densityCutoff=0.0
- Create ARC file of structures above a specified density.
- --ec, --energyCutoff=0.0
- Create ARC file of structures within a specified energy of the lowest energy structure.
- --fl, --findLowest=0
- Return the n lowest energies from an ARC/PDB file.
- -g, --gradient
- Compute the atomic gradient as well as energy.
- -h, --help
- Print command help and exit.
- --in, --inertia
- Print out the moments of inertia.
- -m, --moments
- Print out electrostatic moments.
- --pb, --printBondedTerms
- Print all bonded energy terms.
- --pd, --printDihedral=<dihedralAtoms>
- Atom indices to print dihedral angle values.
- --rg, --gyrate
- Print out the radius of gyration.
- -v, --verbose
- Print out all energy components for each snapshot.
- -V, --version
- Print the Force Field X version and exit.
Atom Selection Options
- --aa, --active=<selection>
- Ranges of active atoms [NONE, ALL, Range(s): 1-3,6-N].
- --ia, --inactive=<selection>
- Ranges of inactive atoms [NONE, ALL, Range(s): 1-3,6-N].
Alchemical Options
- --ac, --alchemicalAtoms=<selection>
- Specify alchemical atoms [ALL, NONE, Range(s): 1-3,6-N].
- --acRes, --alchemicalResidues=<selection>
- Specify alchemical residues by chain and residue number [A4,B21]
- -l, --lambda=-1
- Initial lambda value.
- --uc, --unchargedAtoms=<selection>
- Specify atoms without electrostatics [ALL, NONE, Range(s): 1-3,6-N].
Alchemical Options for Dual and Quad Topologies
- --ac2, --alchemicalAtoms2=<selection>
- Specify alchemical atoms for the 2nd topology [ALL, NONE, Range(s): 1-3,6-N].
- --acRes2, --alchemicalResidues2=<selection>
- Specify alchemical residues by chain and residue number for the 2nd topology [A4,B21]
- --np, --nParallel=1
- Number of topologies to evaluate in parallel
- --sf, --switchingFunction=1.0
- Switching function to use for dual topology: options are TRIG, MULT, or a number (original behavior with specified lambda exponent)
- --uaA, --unsharedA=-1
- Unshared atoms in the A dual topology (e.g. 1-24.32-65).
- --uaB, --unsharedB=-1
- Unshared atoms in the B dual topology (e.g. 1-24.32-65).
- --uc2, --unchargedAtoms2=<selection>
- Specify atoms without electrostatics for the 2nd topology [ALL, NONE, Range(s): 1-3,6-N].