• How do I get MMC? MMC can be downloaded from http://inka.mssm.edu/~mezei/mmc.

• How do I get help in using MMC? If the manual ( http://inka.mssm.edu/~mezei/mmc/html) does not offer the answer, send e-mail to Mihaly.Mezei@mssm.edu, attach your input and output files and a copy of the error messages.

• What statistical ensembles can MMC simulate? MMC can simulate systems in the canonical, grand-canonical and isothermal-isobaric ensembles.

• What kind of systems can MMC simulate? MMC can simulate an arbitrary collection of molecules that can be translated and rotated independently and have their torsion angles varied.

• What does the concept of the solvent cover for MMC? The concept of solvent for MMC covers a single type of molecule and generally the system is assumed to contain many of these. Several water models (e.g., TIP3P, TIP4P, SPC) are built in but users can also define a solvent molecule of their own. However, solvent molecules are without internal degrees of freedom and considered as a single residue, allowing the use of simpler, therefore faster code to use for evaluating their interactions.

• What does the concept of the solute cover for MMC? MMC considers everything that is not solvent to be the solute. It can be a collection of different molecules that can be translated and rotated independently and can have variable torsion angles. Solute molecules can also be broken into residues (also called groups).

• What does the solute stepsize read with the STEP key refer to? This quantity (a remnant of the early stage of developments when formamide was a complex solute) is of relevance when the solute is a single molecule and thus it can be treated much like a solvent molecule.

• How does one specify the solute molecules that are to be moved and their stepsizes? The key PARD specifies this information.

• How does one specify the torsion angles that are to be moved and their stepsize? The key TORD specifies the torsion angles that MMC will move. It is also possible to let MMC find all the torsions that can be sampled. The key PART selects the torsion sampling strategy.

• How does MMC work without a topology file? MMC requires a sample of each type of molecule that is part of the solute (read by the key SLTA). It deduces the molecular topology by establishing the connectivity from the interatomic distances.

• What kind of potential functions does MMC support? MMC has built-in non-bonded parameters for Charmm, Amber, OPLS, Gromos/Gromacs and Clementi's potentials and supports the EPEN format as well. Atom types not built in can be defined by the users in any of these forms. Torsion potential parameters can be established by reading in the parameter file of the potential type chosen.

• How does one import a system into MMC from other programs' syntax? Beside its internal file format, MMC can read in configurations in Charmm and PDB formats. For the definition of the system, the program Simulaid (downloadable from http://inka.mssm.edu/~mezei/simulaid) can generate the solute description file (.slt file) based on the atom and residue names using either it own list or the topology file used to define the solute in Charmm, Amber or Gromos/Gromacs.

• For free energy calculation over a creation/annihilation path, do the two solutes have to have the same number of atoms? No. When using the FREE TICA option the two solutes can have number of atoms, specified by the SLTA key.

• How do I find errors in my input?
  • Read carefuly the error message
  • Take advantage of keys for additional output (e.g., PLBP, BNDL, REPT) to see how MMC 'sees' your inputted systems.
  • One frequent source of error is the use of incorrect format in formatted inputs. The PRNT DETL option will echo all data read with formatted input, allowing you to spot format errors.
  • MMC is quite lenient during the input. This has the advantage of allowing to detect several errors with one run, but has the drawback that one error may have additional consequences that are not at all obvious (including crashes). Thus, when 'weird' errors are printed, it is important to check the output file for all the WARNINGs, STRONG WARNINGs and ERRORs, fix all errors that are clear and try again.

• Is MMC parallelized?

  There are selected features that are parallelized: solvent-solvent and solute-solvent energy calculations, grand-canonical ensembnle calculations and calculation of the excess chemical potential with the Widom insertion method. However, except for the Widom-insertion calculations, acceptable performance requires either shared memory architecture or that all CPUs be on the same node.

• How can I visualize the results?
  1. You can use WCNF PDB to write a PDB file of the lats configuration
  2. You can use Amber of Charmm trajectory format (unless you run in the grand-canonical ensemble). Both of these formats are recognized by most visualization software.
  3. For GCE runs, you can use the program Simulaid to unpack the trajectory into PDB files.

• Can I set up the MOND box to be an area in the simulation cell not enclosing the solute?

  Yes

Last modified: 01/10/12