Request for information about OOPSE code

[Dan Gezelter]

>
> Hello,

Greetings.

> 1. Can OOPSE incorporate more sophisticated, directional or  
> multibody potentials for performing MD
> simulations of atoms (like those of GPT theory, for example)?

Well, OOPSE can't do GPT right now.  The framework for our metals code
is a two-pass code that first calculates local density and then makes
a second pass to compute the forces.  This portion of the code has been
parallelized, and since there are strong similarities in the  
structures of
codes that perform multibody potential calculations, OOPSE may a good
starting point for implementing a more complicated potential.  We  
currently
include two different multibody potentials (EAM, Sutton-Chen).  Adding
directional multibody potentials (like MEAM) is on our "To Do" list, but
we haven't gotten it done yet.  GPT would be, I think, a bit harder to
implement in OOPSE because it has explicit four-body terms.

If you decide to use our code, we'd be happy to help you out with
getting your potential of interest into OOPSE.

> 2. Will the program be able to simulate systems consisting of  
> proteins of biological interest, using one of the
> commonly accepted force fields?

All the functional forms and infrastructure are already present in OOPSE
to do protein simulations, and readers for the Amber and CHARMM force  
field files
are very high priorities for me.

> 3. How does the performance of OOPSE compare with other MD codes?

We're pretty fast.  Probably not as fast as Gromacs, but we haven't  
pushed
the limits yet (i.e. spline fits for LJ forces, etc.)

> 4. What are the most recent publications which illustrate the  
> code's performance and capabilities?

Computational Free Energy Studies of a New Ice Polymorph Which  
Exhibits Greater Stability than Ice Ih
Christopher J. Fennell and J. Daniel Gezelter
J. Chem. Theory Comput.; 2005; 1(4) pp 662 - 667;

Breathing Mode Dynamics and Elastic Properties of Gold Nanoparticles
Charles F. Vardeman II, Patrick F. Conforti, Megan M. Sprague, and J.  
Daniel Gezelter
J. Phys. Chem. B; 2005; 109(35) pp 16695 - 16699;

OOPSE: An Object-Oriented Parallel Simulation Engine for Molecular  
Dynamics
Matthew A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher J.  
Fennell and J. Daniel Gezelter
J. Comput. Chem. 26, pp. 252-271 (2005).

On the structural and transport properties of the soft sticky dipole  
(SSD) and related single point water models
Christopher J. Fennell and J. Daniel Gezelter
J. Chem. Phys. 120, pp. 9175-9184 (2004).

Size Dependent Spontaneous Alloying of Au-Ag Nanoparticles
Tomohiro Shibata, Bruce A. Bunker, Zhenyuan Zhang, Dan Meisel,  
Charles F. Vardeman II, and J. Daniel Gezelter,
J. Am. Chem. Soc. 124, 11989-11996 (2002).

The code was evolving dramatically during this period, however, so  
the newest version
is a lot more capable and efficient than some of the earlier versions.

Best regards,

  --Dan Gezelter

***********************************************
   J. Daniel Gezelter
   Associate Professor
   Department of Chemistry and Biochemistry
   251 Nieuwland Science Hall
   University of Notre Dame
   Notre Dame, IN 46556-5670

   phone:  +1 (574) 631-7595
   fax:    +1 (574) 631-6652
   e-mail: gezelter at nd.edu
   web:    http://www.nd.edu/~gezelter
************************************************