MOIL programming

Elber R, Roitberg A, Simmerling C, Goldstein R, Li H, Verkhivker G, Kaesar C, Zhang J, Ulitsky A. 1995. MOIL A program for simnlations of macromolecules. Comp. Phys. Comm. 91 159-189. 

All the calculations described below were done with the program MOIL [28]. Moil is a freely available molecular simulation package with a focus on reaction path and rate calculations. Structures selected from the trajectory described in the previous paragraph were fed into MOIL. They were refined into a detailed SDP from a helix to a coil conformation with the action formnlation of Olender and Elber [29]. The SDP was computed in a rednced snbspace of coarse variables, namely the positions of the C -s of the peptide. We are making the plausible assumption that side chain motions equilibrate more rapidly than backbone degrees of freedom. 

The input file for SDEL, called path.inp in MOIL (Table 1), contains the names for the file rcrd) with the initial guess trajectory (i.e., a binary file with extension pth), and the molecule s connectivity file used to extract the potential parameters for the force field. The connectivity file (with extension wcon) is generated by the program conn in MOIL. 

At the end of a run, the final trajectory is output [file word) with path format. MOIL contains several programs that can be used to analyze the trajectory (computation of radius of gyration, native contacts, secondary structure content, etc). The Windows graphics interface of MOIL can be used to visualize the trajectory. Also, the path format can be converted to a more conventional format like dcd using the ccrd program of MOIL. Dcd files can be open by many molecular visualization programs such as VMD. ... 

J. Zhang, and A. Ulitsky, Comput. Phys. Commun., 91, 159 (1995). Moil—A Program for Simulations of Macromolecules. 

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