MACSIMUS is a free molecular modeling and simulation package maintained by Jiri Kolafa

Quickstart

• Latest release 2024-02-19 with blend V2.4e and cook V3.6s: GitHub or Local ZIP
  (cleaning before the 1st release on GitHub, bug fixes, more examples)
• Quick install under Linux, Windows+CygWin, or Windows/WSL:
  • unzip the archive (it includes path "macsimus/")
  • from "macsimus/" run shell script "./install.sh"
  • follow instructions (install packages as recommended, compile)
• MACSIMUS is a free software. See the read me file for details.
• The manual (in PDF).

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 University of Chemistry and 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 ASPC and PSPC
  • 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

* WARNING: between 2022-05-20 and 2024-02-18, file sim/intrapot.c was wrong in some versions (because a bad one was on a notebook and a good one at work) causing omitting the virial of non-bonded forces in pressure. Thus, in * versions, file sim/intrapot.c should be replaced by a new one.

• Release 2024-02-07 with blend V2.4e and cook V3.6r (bug fixes: enthalpy in NVT/NVE, el. background in FREEBC control, pakcp)
• Release 2024-01-08 with blend V2.4e and cook V3.6q (small fix for SLAB/evaporate)
• Release 2023-11-06 with blend V2.4e and cook V3.6o (Hoover NPT, ⟨(P_cfg−P)⋅V⟩ added)
• * Release 2023-09-28 with blend V2.4e and cook V3.6m (blend -b fixed, code cleaned)
• * Release 2023-07-06 with blend V2.4d and cook V3.6m (calculation of kinetic properties of a molecule having evaporated)
• Release 2023-06-16 with blend V2.4d and cook V3.6l (magnetic field, drift/corr rehacked, angular and linear momentum of clusters, -k0, bug fixes)
• Release 2022-10-27 with blend V2.4d and cook V3.6j (bugs fixed, plbsmooth added)
• Release 2022-06-30 with blend V2.4d and cook V3.6f (Ballenegger-Arnold-Cerda correction for Ewald slab + charged system added)
• * Release 2022-06-24 with blend V2.4d and cook V3.6e (spaces and some special chars now allowed in PATH (useful in WSL), bugs fixed, improvements)
• * Release 2022-06-07 with blend V2.4d and cook V3.6b (trickle, droplet etc. geometry, support for evaporated particles, load cfg with diffrent numbers of atoms, Ewald background, ANCHOR, bugs fixed, polishing)
• Release 2021-11-15 with blend V2.4d and cook V3.5d (fixed: cluster analysis, plbmerge, evu ha, a, a_T, a_G, a_J, comment, field, install, added cook -d-#)
• Release 2021-09-14 with blend V2.4d and cook V3.5b (linking duplicate fixed, FMT in utilities)
• Release 2021-06-20 with blend V2.4d and cook V3.4r (spectrum improved, small fixes)
• Release 2021-05-19 with blend V2.4d and cook V3.4r (cl.mincluster added)
• Release 2021-03-04 with blend V2.4c and cook V3.4q (plbmerge fixed, export Nose-Hoover xi shifted time fixed)
• Release 2021-02-26 with blend V2.4b and cook V3.4p (Export of Drude positions, true charge density profile with Gaussian charges, MTK λ export and manual update)
• Release 2021-01-30 with blend V2.4b and cook V3.4m (enthalpy: bug fixed, more info printed)
• Release 2021-01-04 with blend V2.4b and cook V3.4k (bugs fixed)
• Release 2020-11-13 with blend V2.4b and cook V3.4j (NPT documentation, velocity playback option, centered box; utilities: molren, line, oneline)
• Release 2020-09-19 with blend V2.4b and cook V3.4g (support for oscillating external electric field)
• Release 2020-08-07 with blend V2.4a and cook V3.4e (small changes, see history.txt)
• Release 2020-02-28 with blend V2.4a and cook V3.4b (small bugs fixed, ECC more transparent)
• Release 2019-12-23 with blend V2.4a and cook V3.3o (format of cp changed: showcp shows time in ps as t-axis, bugs fixed)
• Release 2019-11-03 with blend V2.4a and cook V3.3l (Bussi thermostat, show bug fixed)
• Release 2019-10-08 with blend V2.4a and cook V3.3k (5/2019 SI definition, ECC support, gol-files removed etc.)
• Release 2019-08-01 with blend V2.3e and cook V3.3g (CLUSTER etc. small improvements)
• Release 2019-04-18 with blend V2.3e and cook V3.3d (Improved: neutrality test, cfg2asc, asc2cfg, control od plots spawned by rdfg, showcp. Small mem leak fixed.)
• Release 2019-01-26 with blend V2.3e, cook V3.3a and show 2.1a (walls rehacked, small changes and fixes)
• Release 2018-12-12 with blend V2.3e, cook V3.2d, show V2.0m (show: bug fixed and better marking)
• Release 2018-09-13 with blend V2.3e and cook V3.2a (numbers of degrees of freedom reconsidered, plot improved, fortran numbers fixed)
• Release 2018-06-15 with blend V2.3e and cook V3.1m (normal mode vibrations with general constraints)
• Release 2018-05-04 with blend V2.3e and cook V3.1j (bug fixes)
• Release 2017-12-21 with blend V2.3e and cook V3.1f (cluster analysis in show)
• Release 2017-12-04 with blend V2.3e and cook V3.1f (periodic sum added, bugs fixed)
• Release 2017-07-10 with blend V2.3b and cook V3.0i (bug in POLAR of V3.0a fixed)
• Release 2017-05-29 with blend V2.3b, cook V3.0e, show 2.0f (cross-section of clusters, changed simulate/reread logic (for clusters, cross-section, diffusion, conductivity...))
• Release 2017-01-31 with blend V2.3a and cook V2.9e (GUI changed to home-made X11)
• Release 2016-08-05 with blend V2.2i and cook V2.9e (last version with the gtk-based GUI)
• Release 2016-03-14 with blend V2.2h and cook V2.8h (Fourier-expansion slab cutoff corrections)
• Release 2015-12-17 with blend V2.2h and cook V2.8f (V(t) control, inertia/gyration matrix in blend)
• Release 2015-09-17 with blend V2.2g and cook V2.8a (BK3-compatible ions [cook only], cleaving update, σ_ij fitting, CODATA 2015, variable poteps)
• Release 2015-01-08 with blend V2.2g and cook V2.7q (velocity shift)
• Release 2014-06-13 with blend V2.2g and cook V2.7p (Gaussian charges)
• Release 2013-08-28 with blend V2.2g and cook V2.7l (Tstop added to data, Ekin added to cp)
• Release 2013-04-03 with blend V2.2g and cook V2.7k (bug fixed: normal modes of vibrations failure in some range of masses)
• Release 2012-12-11 with blend V2.2g and cook V2.7j (bug fixed: Ptens with Ewald dipole, enthalpy, saturation autoset, format of *.g and key="rdf","cn"; PSPC(3) also with Verlet, normal vibrations may call octave)
• Release 2012-06-28 with blend V2.2g and cook V2.7f (better linked-cell-list setup)
• Release 2012-06-01 with blend V2.2g and cook V2.7c (normal mode vibrations incl. constrained models, shifted erfc splines to improve num. derivatives)
• Release 2012-03-30 with blend V2.2f and cook V2.7a (MTK thermostat+barostat, more ices)
• Release 2011-07-15 with blend V2.2d and cook V2.6h (MSD analysis, control changes)
• Release 2011-06-06 with blend V2.2d and cook V2.6g (small fixes, harmonics and full corr.f. revisited)
• Release 2011-04-26 with blend V2.2d and cook V2.6f (fluctuating charge, better permittivity etc.)
• Release 2011-02-22 with blend V2.2d and cook V2.6e (cleaving, Langevin, error estimates, bugs fixed 2011-03-31)
• Release 2010-10-26 with blend V2.2b and cook V2.6a (new site-site interface, Buckingham extended, GUI for blend)
• Release 2010-06-01 with blend V2.1l and cook V2.5e (diffusivity in NPT)
• Release 2010-03-15 with blend V2.1k and cook V2.5b (shared memory parallel via pthreads; fixed small memory leak)

[Department homepage] [J. Kolafa private homepage]