NAME

singlept - compute the potential energy value for a given coordinates


SYNOPSIS

singlept--help ] [ --version ] [ --verbose num ] [ --vdw14 num ] [ --eel14 num ] [ --diel-lin num ] [ --diel-const num ] [ --cutoff num ] [ --gradient ] [ --numgrad ] file.top file.crd


DESCRIPTION

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.


OPTIONS

--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:

  1. Be really quiet. Do not print anything. Well, with this option this program is really unusable.

  2. Print the total value of the potential energy only

  3. Print the following message:

     ### Total value of potential energy:   <number>
    

  4. Print the total value of the potential energy as well as the summary values for each type of interaction energy function consists of.

  5. 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 particular interaction.

--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.

--gradient
Prints the gradient values instead of potential energy value.

--numgrad
Prints the gradient values computed numerically instead of explicitly computed gradient. This can probably used for testing as it is slower than --gradient


COPYRIGHT

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.


AUTHORS

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 Mejzlík.


BUGS

Probably there are some. Send the bugfixes (prefered form is a diff -u output) and bug-reports to Jan ``Yenya'' Kasprzak (kas@fi.muni.cz).


SEE ALSO

opal_singlept_t(1), opal(1)