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Minimize(1) Manual Page


Minimize - Run L-BFGS minimization on a system.


Minimize [-hV] [--aa=<selection>] [--ac=<selection>] [--ac2=<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…​


Run L-BFGS minimization on a system.


-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.


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].



Atomic coordinate files in PDB or XYZ format.