MOIL: Molecular Dynamics and Modeling
Software

HIV-RT coordinates displayed with the program Pymol |

Moil^{1}
(Molecular Operations In Life) is a suite of molecular dynamics programs that supports the usual set
of tools for molecular modeling by classical mechanics (see Introduction to Molecular Dynamics). Examples are energy
calculations (program energy), energy minimization (mini_pwl and mini_tn), and molecular dynamics (dyna and dynaopt). Source code and execution files are available for download (DOWNLOAD).

dynaopt^{2} is a
recent optimized version of the moil code that runs on a GPU and on
shared memory systems. On a single node (with GPU) dynaopt is
comparable in speed to the fastest codes out there while retaining excellent energy conservation.

Graphic user interface is supported (moil.tcl) written in tcl.tk and a visualization program zmoil is included in the release (currently version 12).

Moil allows for reasonably straightforward conversion of PDB files to
computable datasets (coordinate and energy templates) through moil.tcl.

More advanced applications are also supported, such as Landau-Zener curve crossing model^{3}, replica exchange^{4}, free energy calculations of mutants^{5}, a coarse grained potential^{6} and "plastic" networks^{7}.

Moil includes a number of novel algorithms developed in our group. For example, Locally Enhanced Sampling (LES)^{8}.

A major research emphasis in Moil is of kinetics and a number of programs are available through moil to compute reaction
pathways, long time dynamics, and rates. Minimum energy paths are
computed by the program chmin^{9} and SDP^{10}. Approximate long time trajectories are computed with SDEL^{11}. Minimum free energy pathways are computed with the string method^{12} (MFEP).

A significant research effort of the last few years focuses on the method of Milestoning and Directional MIlestoning (DiM)^{13}
in which transitions between interfaces at a reaction space are
recorded and used to generate a non-Markovian model that is solved
esentially analytically. The non-Markovian model extends
simulations even to hours of physical times ^{14} . DiM runs consist of three sequential stages: dim_prepare, dim_sample and dim_run.

RECENT BENCHMARKS

Time of nonbonded real space force calculation as a function of the number of atoms (time per atom shown) on a GTX480 GPU. Seven test systems are used (in parenthesis the number of atoms): Pepta (2690), TRPzipper (5487), Helix (20187), DHFR (23536), DOPC/NaCl solution (38802), 1IHF (91765), Myosin (99905). See ^{15} for more details. |

DOWNLOAD: Details about obtaining the latest source code from svn are available on our wiki, or you may download prebuilt binary packages (including source code) here:

The code is in the public domain. Any portion of
it or the whole code can be used in any capacity. The only requirement is that references will be
made to the original authors in any study that uses MOIL. New codes
that build on MOIL should detail the extent of use and include in their
release notes a statement to that effect.

DOCUMENTATIONS: can be found in the moil.doc folder of your distribution, or you can look at specific documents here:

- Release Notes
- MOIL documentation
- Introduction to Molecular Dynamics (MD) and MOIL Force Field
- Reaction Path Functionals in MOIL
- zmoil documentation

MOIL TUTORIALS AND TRAINING WORKSHOP FILES:

- Getting
Started with MD

- Getting Started with Reaction Paths
- An Introduction to Milestoning Theory

- Getting Started with Milestoning
- Introduction to MOIL: Computation of Reaction Paths, NAIS Workshop (2012)
- Moil: Milestoning, NAIS Workshop (2012)

REFERENCES