|MOIL - A Public Domain Molecular
We announce the release of a new version of the package for molecular
dynamics and modeling MOIL1
- MOIL11. The complete source code
is included. Ready execution files are available for Windows XP, Mac OS/X,
and Linux (Fedora). The code is in the public domain. You may use it or any
portion of it in any way you like. 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 the first paragraph of this message.
Moil supports the usual set of tools for molecular modeling by classical
mechanics, including energy calculations, energy minimization, molecular
dynamics, and more. Code is available to simulate curve crossing within the
Landau Zener model. Moil allows for reasonably straightforward conversion of
PDB files to computable datasets (coordinate and energy templates).
Besides "Standard" applications MOIL evolves around the research in Ron
Elber’s laboratory. Examples are the Locally Enhanced Sampling Approach2
and reaction path and long time dynamics algorithms 3
that are based on action optimization. Also included the recently developed
Milestoning approach for the calculation of kinetics and thermodynamics
along a reaction coordinate4.
The integration of a coarse-grained model into moil is yet another new
feature of MOIL11.
Numerous examples and templates are included in the moil/moil.test
directory. Documentations are in moil/moil.doc. A dictionary of keywords
used in moil is available at moil/moil.doc/dictionary.txt
Significant new enhancements to the older version(s) include
Get a pre built code
http://clsb.ices.utexas.edu/prebuilt or signed on a SVN server for
continuous updates of source code
A new visualization program (zmoil) for graphic display of individual
structures, dynamics, reaction paths and overlay of multiple structures,
read PDB CRD DCD and (MOIL specific) PTH formatted files. (by Thomas Blom
and Baohua Wang)
- Enhanced graphic interface moil.tcl for numerical simulations with
numerous bug fixes. Not all moil modules are supported by the graphic
interface (by Thomas Blom and Baohua
A new coarse-grained model of proteins (two points per amino acid) for
energy, minimization, dynamics and path calculations (by Peter Majek)
- Replica exchange (by Serdal Kirmizialtin)
New code for stochastic optimization of
approximate trajectories with large step (SDEL by Peter Majek)
- Steepest descent path calculation by action optimization (sdp module by
Ron Elber and Peter Majek)
- Milestoning simulations of kinetics (the fp module by Anthony West)
- Implementation of OPLS DNA/RNA force field in addition to OPLS for
proteins and liquid simulations (by Serdal Kirmizialtin)
- Calculation of pressure (by Luca Maragliano)
MOIL11 team: Thomas Blom, Peter Majek, Serdal Kirmizialtin, and Ron Elber
A few references
R. Elber, A. Roitberg, C. Simmerling et al., Computer Physics
Communications 91 (1-3), 159 (1995).
C. Simmerling and R. Elber, Journal of the American Chemical Society
116 (6), 2534 (1994); G. Verkhivker, R.
Elber, and Q. H. Gibson, Journal of the American Chemical Society 114
(20), 7866 (1992); A. Roitberg and R. Elber, Journal of Chemical Physics
95 (12), 9277 (1991); R. Elber and M.
Karplus, Journal of the American Chemical Society 112
(25), 9161 (1990).
W. Nowak, R. Czerminski, and R. Elber, Journal of the American Chemical
Society 113 (15), 5627 (1991); R.
Czerminski and R. Elber, International Journal of Quantum Chemistry, 167 (1990);
R. Olender and R. Elber, Theochem-Journal of Molecular Structure 398,
63 (1997); P. Majek, H. Weinstein, and R. Elber, Pathways of conformational
transition in proteins. (2007).
A. M. A. West, R. Elber, and D. Shalloway, Journal of Chemical Physics
126 (14) (2007).