**--help**-
Prints out help message and exits.
**--version**-
Prints out the version of the program and exits.
**--verbose number**-
Sets the verbosity level. The levels have the following meaning:
Minimum is <number>

Where the <number> is the value of energy in the local minimum.

**--vdw14 number**-
Sets the scaling parameter for van der Waals part of the 1-4 interactions.
The default value is 2.0.
**--eel14 number**-
Sets the scaling parameter for the electrostatic part of the 1-4
interactions. The default value is 1.2.
**--diel-lin number**-
Sets the linear part of dielectric funtion. The default value s 0.0 which
means to simulate the force field without the solvent. Set this to 4.0 to
simulate water. This option is used together with the next one.
**--diel-const number**-
Sets the constant part of dielectric function. The default value is 1.0
which means to simulate the force field without the solvent. Set this to
4.0 to simulate water. This option is used together with the previous one.
**--cutoff number**-
Sets the cutoff parameter for the 1991 force field. The cutoff means that
the nonbonded interactions for atoms from different residues that have
distance greater than the cutoff are not evaluated. This is used in Amber
1991 force field for reaching some speedup. I don't think it speeds up
Opal, but I have included this for compatibility. The default is not to use
cutoff, i.e. +infinity.
**--begin-coords filename.crd**-
The coordinates from which the minimization is started. If this option is
not given,
*lmin*generated the starting coordinates randomly. **--outfile filename.crd**-
The coordinates of the local minimum are written into this file at the end
of the program.
**--seed number**-
The random number generator seed. The random number generator is set to use
this seed for generating of random coordinates. This option is usable only
when
**--begin-coords**is not given. **--accuracy number**-
The accuracy of the local minimizing procedure. The default is 1.0e-5. This
number controls when the minimizing stops.
**--numgrad**-
The gradient values computed numerically instead of explicitly computed
gradient. This can probably used for testing as it is slower than default
behavior.

`diff -u`

output) and bug-reports to Jan ``Yenya'' Kasprzak (kas@fi.muni.cz).
A not-exactly-bug: I am looking for a good local minimization routine written in C so that Opal can be compiled without the Fortran compiler.

*http://www.nag.co.uk/* - The Numerical Algorithms Group, Ltd.

*http://www.netlib.org/blas* - The Basic Linear Algebra Subprograms.