Opal - system for molecular modelling
Opal is a still-growing system for molecular modelling. It implements the Amber 4.1 potential energy funciton (aka force field) and it is compatbile with
*.top files (describes the structure of the molecule) and *.crd files (contains the three-dimensional coordinates of molecule's atoms).
- It is written in C.
It can be easily modified.
- It is free.
You can modify it and distribute it under the terms of GPL (see the section
Copyright near the end of this file.
- It is portable.
Opal has been tested on different platforms, including the 64-bit ones. It
has pain-less configuration via the configure script (generated by the autoconf(1)).
- It is fast.
Is it really fast?
There is no program named opal in the Opal system. Instead of this, Opal consists of independent programs
- for single-point computations, local and global minimization and a few
other utilities. You can use these programs directly or write your own
front-end (usually by modifying the main() function of one of the Opal's programs). For information on the Opal
internals (data structures and subroutines) see
The utilities Opal consists of are:
This program can evaluate the potential energy for the molecule and the
given coordinates as well as the gradient of the force field in this point
of the potential hypersurface. It has several levels of verbosity and it
can print the energy of each interaction the force field consists of. See opal_singlept(1) for details.
This program is similar to previous. The difference is it can compute the
transformed (smoothed) value of the potential energy function. To use this
program you must pre-compute the tables describing the transformed function
using ??? first. See singlept_t for details.
Local minimization program. This program can find the local minimum of the
potential energy function corresponding to a given start coordinates. It
can use the explicit or numerically-computed gradient. See lmin
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
There are definitively bugs in Opal. The
$(STABLE_PROGS) (see the Makefile) should be more stable and bug-free. Send the bugfixes (prefered form is a
diff -u output) and bug-reports to Jan ``Yenya'' Kasprzak (email@example.com).
- Amber 4.1 WWW site
- Opal WWW site
- Other manual pages:
opal_singlept, opal_lmin, opal_gmin, opal_internals.