Minimize(1) Manual Page

Name

Minimize - Run L-BFGS minimization on a system.

Synopsis

Minimize [-hV] [--aa=<selection>] [--aa=<selection>] [--ac=<selection>] [--ac=<selection>] [--ac2=<selection>] [--ac2=<selection>] [-e=1.0] [-e=1.0] [-I=Unlimited] [-I=Unlimited] [--ia=<selection>] [--ia=<selection>] [-l=-1] [-l=-1] [--nbfgs=7] [--nbfgs=7] [--np=1] [--np=1] [--sf=1.0] [--sf=1.0] [--uaA=-1] [--uaA=-1] [--uaB=-1] [--uaB=-1] [--uc=<selection>] [--uc=<selection>] [--uc2=<selection>] [--uc2=<selection>] files…

Description

Run L-BFGS minimization on a system.

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].
-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].
--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].

Arguments

files…: Atomic coordinate files in PDB or XYZ format.