New MOIL release (MOIL9)

http://cbsu.tc.cornell.edu/software/moil

Moil is yet another molecular dynamics package that performs energy related calculations. In addition to the common applications of energy, minimization, dynamics, and free energy differences of biological molecules, MOIL has a number of unique features developed at the group of Ron Elber. Below we highlight a few of them

1. Long time dynamics algorithms – the stochastic difference equation

Our recent methodology to extend significantly the time scale of simulations. Serial and parallel code is now available in the sdel module

[1] Alfredo Cárdenas and Ron Elber, “Kinetics of Cytochrome C Folding: Atomically Detailed Simulations”, Proteins, Structure Function and Genetics, 51,245-257(2003)

[2] Avijit Ghosh, Ron Elber, and Harold Scheraga, “An atomically detailed study of the folding pathways of Protein A with the Stochastic Difference Equation”, Proc. Natl. Acad. Sci., 99,10394-10398(2002).

[3] Ron Elber, Avijit Ghosh, Alfredo Cárdenas and Harry Stern, ”Bridging the gap between reaction pathways, long time dynamics and calculation of rates”, Advances in Chemical Physics, 126,93-129(2003)

2. Windows 2000 graphic user interface, cmoil graphic display program, and serial and parallel code for Windows clusters

The current version includes a graphic interface for Windows 2000 environment, and a molecular display program cmoil (Windows 2000 again)

3. Locally Enhance Sampling

Moil includes options to perform LES (Locally Enhanced Sampling) simulations. For sample of LES references see:

[1] C. Simmerling and R. Elber, "Hydrophobic "collapse" in a cyclic hexapeptide: Computer simulations of CHDLFC and CAAAAC in water", J. Amer. Chem. Soc. 116, 2534 (1994).

[2] A. Roitberg and R. Elber, "Modeling side chains in peptides and proteins: Application of the Locally Enhanced Sampling (LES) and the simulated annealing methods to find minimum energy conformations", J. Chem. Phys. 95, 9277 (1991).

[3] R. Elber and M. Karplus, "Enhanced sampling in molecular dynamics: Use of the Time-Dependent Hartree approximation for a simulation of carbon monoxide diffusion through myoglobin", J. Amer. Chem. Soc., 112, 9161 (1990).

The new code also includes implementation of the AMBER99 force field for Proteins and DNA (in addition to AMBER/OPLS extended atom model) and a generalized Born model.

Have fun,

Current moil team (alphabetic order)

Alfredo Cardenas, Ron Elber, Ileana Stoica, Amena Siddiqi, and Baohua Wang (Karunseh Aurora helped in the testing of DNA parameters)

Past contributors (alphabetic order)

Chyung Choi, Robert Goldstein, Avijit Ghosh, Chen Keasar, Haiying Li, Jaroslaw Meller, Debasisa Mohanty , Roberto Olender, Adrian Roitberg, Danuta Rojewska, Carlos Simmerling, Koneshan Siva, Alex Ulitsky, Gennady Verkhivker, Yael Weinbach, Veaceslav Zaloj