Frequently asked questions about MMC
- How do I get MMC?
MMC can be downloaded from
- How do I get help in using MMC?
If the manual (https://mezeim01.u.hpc.mssm.edu/mmc/html) does not offer
the answer, send e-mail to
Mihaly.Mezei@mssm.edu, attach your input and output files.
- How do I use an .slt file that is using the old (4-character pf label)
format? Replace MMC with MMC4 in the SLTA line or
to convert it to the new format.
- What statistical ensembles can MMC simulate?
MMC can simulate systems in the canonical, grand-canonical and
- 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
- 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, TIP5P, 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
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 stepsize?
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 with the
PMOD key. Also, a CHARMM
parameter file can be read with the PFRD key.
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'
Beside its internal file format,
MMC can read in configurations in Charmm and PDB formats.
For the definition of the system, the program
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
- How do I find errors in my input?
- Take advantage of keys for additional output (e.g.,
REPT) to see how MMC 'sees' your
- One common source of error is the use of incorrect format in
The PRNT DETL option will echo
all data read with formatted input, allowing you to spot format errors.
- When MMC discovers an error in the input it generally continues reading
and only stops when the run is about to start. 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.
If you have a question to add to this list, send an e-mail to
Last modified: 06/14/2016