Force Field XMinimize(1)
Synopsis
Minimize [-hV] [--aa=<selection>] [--ac=<selection>] [--ac2=<selection>] [--acRes=<selection>] [--acRes2=<selection>] [-e=1.0] [-I=Unlimited] [--ia=<selection>] [-l=-1] [--nbfgs=7] [--np=1] [--sf=1.0] [--uaA=-1] [--uaB=-1] [--uc=<selection>] [--uc2=<selection>] files…
Options
- -h, --help
- Print command help and exit.
- -V, --version
- Print the Force Field X version and exit.
Minimization Options
- -e, --eps=1.0
- Convergence criteria.
- -I, --iterations=Unlimited
- Number of minimization steps.
- --nbfgs=7
- The number of correction vectors used by the L-BFGS optimization routine (0 for steepest-decent).
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].