MACSIMUS is a free molecular modeling and simulation package maintained
by Jiri Kolafa
Quickstart
History
Project MACSIMUS (MACromolecule SIMUlation Software) started in 1991 in
the professor Perram's group at Odense University, Denmark, under name
PROSIS (PROtein SImulation Software), and continued at
MIP,
Theoretical Chemistry at Northwestern University, and the
Institute of Chemical Process Fundamentals.
Now at the Department of Physical Chemistry
of the
Institute of Chemical Technology, Prague,
it is developed towards fluid simulations, ionic systems, surface
phenomena, and polarizability.
Features
- pdb, converter from the PDB format:
- selection of charged states
- residue and pattern replacements, patches
- blend, force field builder and energy minimizer with many features:
- essential dynamics
- normal mode vibrations
- simple molecule editor
- rmsd, inertia matrix, and internal angle analysis
- second virial coefficient
- several models of dipolar polarizability
- cook, a family of molecular dynamics programs in
different boundary conditions supporting:
- SHAKE and Lagrangian constraint dynamics
- linked cell list method
- Ewald summation or cut-off electrostatics
- several models of dipolar polarizability with special integrator
- full pressure tensor calculation (with polarizability, constraints, Ewald)
- surface tension via pressure tensor or virtual area method
- virial pressure and virtual volume change
- radial distrubution functions
- structure factors
- dihedral angle distributions
- cross sections
- optimized water models
- radii of gyration
- shear viscosity calculations
- diffusion coefficients, bulk conductivity
- parallel support for both shared-memory machines and MPI
- show, molecule and trajectory viewer:
- matching of two configurations
- output in two ray tracer formats (NFF and PovRay)
- showing backbones, shells of water molecules, cross sections, etc.
- output of Z-buffer for stereograms
- analysis of simulation results:
- convergence profiles
- statistical errors and time correlation functions
- Ramachandran plot
- tools to work with trajectories
- spectra (with FFT for any factorization of the number of points, not only 2n)
- and general utilities:
- plot: plot graph (with formulas, mouse-controlled zoom, ...)
- command-prompt oriented spreadsheet (I love command prompt...)
- start: start application according to file extension (for
those who love the shell and hate Windows and Gnome etc.)
- sortcite: sort LaTeX citations as they are first
referenced
The package is written in ANSI C. Graphics (blend, show,
and some utilities) is available for basic X11 without any other
requirements.
Old versions
[Department homepage]
[Software page]
[J. Kolafa professional homepage]
[J. Kolafa private homepage]