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
- Release 2010-02-06 with blend V2.1h, cook V2.4n, and show V1.0c (bug pressure tensor fixed)
- WARNING: cook V2.4m has incorrect pressure tensor (fixed in V2.4n above)
- Release 2009-11-30 with blend V2.1f, cook V2.4l, and show V1.0b (H-bonds implemented to show)
- Release 2009-11-18 blend V2.1f and cook V2.4l
- Release 2009-07-31 blend V2.1d and cook V 2.4i (example on melting NaCl and small improvements)
- Release 2009-06-11 blend V2.1c, cook V2.4h, pdb V1.4b (minor improvements and bug fixes)
- Release 2009-05-18 blend V2.1b, cook V2.4g (second virial, plb writing logic)
- Release 2009-04-07 blend V2.1a, cook V2.4f (pressure tensor, improved Ewald, auto constraints, and more)
- Release 2008-10-08 blend V2.0q, cook V2.3.c (rectangular box, slab geometry, Widom and scaled-insertion, cook configurator, etc.)
- Release 2007-03-02 blend V2.0m, cook V2.1a (rectangular box, slab geometry, Widom...)
WARNING:
some versions of MACSIMUS (approx. 2001 – July 2004)
contain in the CHARMM21 force field in file hoh.che and in table
waters in file charmm21.par atom type OT instead of
correct OW. The TIP3P model water is then imprecise. rsd-files and
other versions of CHARMM are OK (they name the TIP3P oxygen OT).
Therefore, if you use CHARMM 21 force field with TIP3P water, check
that in your che- and mol-files for TIP3P water there are OW oxygens,
(not OT), and recreate the ble-files.
Cook should write this message
species HOH: optimized rigid potential function used
Doublecheck of water models was added to cook.
Very old versions of MACSIMUS can be found at the old MACSIMUS homepage.
[Back to the department homepage]
[Back to the software page]