MOIL: Molecular Dynamics and Modeling Software

HIV reverse transcriptase
HIV-RT coordinates displayed with the program Pymol

Moil1 (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).

dynaopt2 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 model3, replica exchange4,  free energy calculations of mutants5, a coarse grained potential6 and "plastic" networks7.

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 chmin9 and SDP10. Approximate long time trajectories are computed with SDEL11. Minimum free energy pathways are computed with the string method12 (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


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:

MOIL TUTORIALS AND TRAINING WORKSHOP FILES:

MOVIE GALLERY

REFERENCES