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 the Amber's
*.top files (describes the structure of the molecule) and
the*.crd files (contains the three-dimensional coordinates
of molecule's atoms).
Why should I use Opal?
- It is written in C.
It can be easily modified, uses a generic-enough routines to allow
changing the force field function without too much pain. At present
Opal supports two slightly different force fields - first one is generic
AMBER 4.1, and the second one is AMBER 4.1 force field smoothed
by spatial averaging.
- It is free/open source.
You can modify it use it and distribute it under the terms of
GNU General Public License
- It is portable.
Opal has been tested on different platforms, including the 64-bit ones. It
has painless configuration via the configure script
(generated by the autoconf(1)). Opal is developed
mainly on Linux on x86,
but Opal has been successfuly compiled and used at least on
the following platforms: Linux/SPARC, Solaris 2.4 and 2.5, IRIX 5.3 and 6.3.
- It interoperable with AMBER.
Opal can read AMBER's *.top files and read and write
the coordinates into the *.crd files.
- It is fast.
For now, I can say that lmin - an Opal's local minimization
program, can minimize alanine dipeptide in 3.7 seconds on my Linux box,
while sander (a local minimization program from AMBER 4.1)
can do the same in more than seven seconds. I need to add more
exact benchmarking here (for various number of atoms, various
HW platforms, etc).
Among the AMBER 4.1 force field Opal implements the same force
field smoothed by the integral spatial averaging. The transformed
(smoothed) force field can be more easily minimized than the
original force field which has its hypersurface populated
by a large amount of unimportant local minima, slowing down
the global minimization algorithms. The on the smoothed
hypersurface the narrow and unimportant local extremes disappear
and global (or even local) minimization is faster and more effective.
Opal is used by its authors mainly for experiments with the spatial
averaging. If you can read the Czech text, look at the
Jan Kasprzak's master thesis
optimalizace v počítačové chemii (Global Optimization in the Computational
Chemistry) which discusses the effectivity of simulated annealing (SA)
algorithm on the raw AMBER 4.1 force field and the smoothed one.
Parts of the program introduced in this thesis are now incorporated
Opal itself is an open source(tm) software. It can be freely
distributed and used under the terms of the
GNU General Public License
The local minimization procedures distributed with Opal in directory
vmlm is copyrighted by Jorge Moré and cannot be used commercially.
See the file README in the vmlm directory in the Opal
source tree. Jorge Moré permitted distributing and using vmlm
with Opal, so you can use vmlm even in the commercial environment,
but only as a part of Opal.
The BLAS library distributed in opal is freely
distributable and usable, but not under the terms of GPL.
See the BLAS FAQ.
Jan "Yenya" Kasprzak