The singlept program serves for evaluation of the potential energy function and its
gradient at the single point of the potential hypersurface of the given
molecule. This program needs two files - the file.top describes the molecule (potential energy function) itself, and the file.crd contains coordinates of molecule's atoms.
Sets the verbosity level. The levels have the following meaning:
Be really quiet. Do not print anything. Well, with this option this program
is really unusable.
Print the total value of the potential energy only
Print the following message:
### Total value of potential energy: <number>
Print the total value of the potential energy as well as the summary values
for each type of interaction energy function consists of.
Prints detailed report - for each single interaction (bond, angle, torsion
and nonbonded interactions) this program prints all the parameters needed
for the computing of that interaction (bond length, angle or torsional
angle value, distance of nonbonded pair) and the energy value for that
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.
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.
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.
Opal itself is an open source(tm) software. It can be freely distributed and used under the terms of GNU General Public License. The minimization procedures distributed with Opal in directories
vmlm and blas are not freely usable. See their license files for more information.
Opal was created as part of master thesis of Jan ``Yenya'' Kasprzak, who is
the current maintainer of Opal. Some parts of Opal (most notably the lmin program and the function for numerical computing of the gradient) as well
as many bug-fixes and suggestions for improvement were contributed by Petr