MOIL - A Public Domain Molecular
Modeling Software
         
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
  1. Get a pre built code http://clsb.ices.utexas.edu/prebuilt or signed on a SVN server for continuous updates of source code https://wiki.ices.utexas.edu/clsb/wiki
  2. 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)
  3. 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 Wang)
  4. A new coarse-grained model of proteins (two points per amino acid) for energy, minimization, dynamics and path calculations (by Peter Majek)
  5. Replica exchange (by Serdal Kirmizialtin)
  6. New code for stochastic optimization of  approximate trajectories with large step (SDEL by Peter Majek)
  7. Steepest descent path calculation by action optimization (sdp module by Ron Elber and Peter Majek)
  8. Milestoning simulations of kinetics (the fp module by Anthony West)
  9. Implementation of OPLS DNA/RNA force field in addition to OPLS for proteins and liquid simulations (by Serdal Kirmizialtin)
  10. Calculation of pressure (by Luca Maragliano)
 
MOIL11 team: Thomas Blom, Peter Majek, Serdal Kirmizialtin, and Ron Elber
 
A few references

1            R. Elber, A. Roitberg, C. Simmerling et al., Computer Physics Communications 91 (1-3), 159 (1995).

2            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).

3            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).

4            A. M. A. West, R. Elber, and D. Shalloway, Journal of Chemical Physics 126 (14) (2007).

 

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