ZMM is a molecular modeling program for theoretical studies of systems of any complexity: small molecules, peptides, proteins, nucleic acids, and ligand-receptor complexes.

ZMM searches optimal structures in the space of generalized coordinates: torsion angles, bond angles, bond lengths, positions free molecules and ions, and orientation of free molecules. Any generalized coordinate may be kept fixed. Molecules and fragments that are not expected to undergo significant conformational changes may be treated as rigid bodies.

Popular molecular modeling programs usually work in the space of Cartesian coordinates of atoms. During energy minimization of a big system, many Cartesian coordinates-variables move collectively. For example, rotation of a benzene ring around the C-Ph bond in the Cartesian-coordinates space involves collective motion of 33 variables. In the generalized-coordinates space, this rotation involves variation of just one torsion angle. In ZMM, any fragment of a molecular system may be treated as either rigid or flexible. The generalized-coordinates method saves large computational resources if only a small part of a system is considered flexible. Examples are ligand-protein and protein-protein interactions. The savings occur because the sampling space is reduced and because molecular interactions within rigid fragments are not computed.

  • ZMM runs on Windows 2000, XP, 7, 10, Mac-OS, UNIX, and Linux
  • ZMM can be used via the command-line interface
  • ZMM can also be used at Windows via a graphical user interface

Scientific Board

Professor Boris S. Zhorov

McMaster University

Professor Daniel S. Yang

McMaster University

Professor Denis B. Tikhonov

I.M. Sechenov Institute of Evolutionary Physiology and Biochemistry

Ten reasons to try ZMM

Here they are:
  1. ZMM is universal: you can model drugs, peptides, proteins, nucleic acid, and ligand-receptor complexes
  2. ZMM is fast. It minimizes energy in the space of generalized coordinates (Zhorov, 1981; Zhorov, 1982) and employs highly efficient method of Monte Carlo minimization (Li and Scheraga, 1987)
  3. ZMM is flexible: large number of controls can tune ZMM for a specific task
  4. ZMM is user-friendly. It includes a graphic interface MVM and can also be used with any molecular graphics program, e.g. RASMOL and PYMOL
  5. ZMM is easy to use: you can import molecular structure from a PDB file in one command or mutate a protein in one keystroke
  6. ZMM is easy to learn. It includes comprehensive description and hundreds of examples
  7. ZMM integrates 30+ years of experience in molecular modeling of biomolecular systems
  8. 200+ publications on ZMM-based studies are available
  9. ZMM runs under Windows, UNIX, and Linux
  10. Parallel ZMM for UNIX and Linux is available

More about ZMM

ZMM implements various methods for conformational search:

  • Energy minimization in generalized coordinates (Zhorov, 1981, 1983)
  • Nested rotations with building multidimensional grids
  • Monte Carlo minimization (Li & Scheraga, 1987)
  • Monte Carlo minimization (MCM) in the space of scaled collective variables (Noguti & Go, 1985; Maurer et al., 1999)
  • Biased MCM (Abagyan & Totrov, 1994)
  • Nested MCM protocol (unpublished)
  • Stochastically restrainable MCM (unpublished)
  • Computing MC-minimized energy profile of a ligand in a protein (Zhorov and Lin, 2000)
  • Computing multidimensional MC-minimized energy map of a ligand in a protein (unpublished)

ZMM includes well-known force fields:

  • ECEPP/2
  • MM2
  • V.G. Dashevskii (1970)
  • Zhurkin et al. (1983)


ZMM was used as the major modeling tool in 300+ studies, including


Click the followings to download ZMM:

  • ZMM-2022a for Windows
  • ZMM-2022b for Windows
  • ZMM-2022 for GNU/Linux (x86_64)
  • ZMM-2022_a for Mac (x86_64)
  • ZMM-2022_b for Mac (x86_64)
  • ZMM-2022 Help file (x86_64)
  • MVM-2022 Help file (x86_64)

  • Contact Us

    ZMM Software Inc.

    65 Mercer Street

    Dundas, Ontario

    Canada L9H 6C7

    Phone 905-962-5139