The PINY_MD simulation package

The PINY_MD(c)* Simulation Package**

Principle Authors: Glenn J. Martyna1 and Mark E. Tuckerman2

1 Dept. of Chemistry, Indiana University, Bloomington, IN 47405.

2 Dept. of Chemistry and Courant Institute, New York University, New York, NY 10003

Other Authors: D. A. Yarne, S. O. Samuelson, A. L. Hughes, Y. Liu, Z. Zhu, M. Diraison, K. Pihakari

*COPYRIGHT 2002: G. J. Martyna (Indiana University), M. L. Klein (University of Pennsylvania), M. E. Tuckerman (New York University). This software is OSI Certified Open Source Software. OSI Certified is a certification mark of the Open Source Initiative. The OSI Certified license selected is the Common Public License

**Please note that this page is under construction -- check back soon for a more complete description of the packag






PINY_MD(c) is a multipurpose, object-oriented molecular simulation package developed as a collaborative effort between Indiana University, New York University and the University of Pennsylvania. PINY_MD(c) is capable of performing a wide variety of molecular dynamics, electronic structure, and geometry optimization calculations. Such capabilities include force-field based (``classical'') simulations on system ranging in complexity from simple molecular liquids (.e.g, water, ammonia, liquid alkanes) and crystals (e.g., ice) to large biomolecular systems such as the HIV-1 protease in solution. Long range electrostatic forces are treated using smooth particle-mesh Ewald summation techniques. Biomolecular systems can be constructed using the code's built-in molecular building tools. In addition, PINY_MD(c) can perform ab initio molecular dynamics and geometry optimization using plane-wave based generalized gradient (GGA) density functional based representations of the electronic structure combined with the Car-Parrinello propagation scheme.

Simulations can be performed in a number of statistical ensembles, including the microcanonical (NVE), canonical (NVT) and isothermal-isobaric (NPT) with isotropic or fully flexible cell variations. Ensembles are generated using well established methodology developed by the principle authors. All molecular dynamics simulation types can be performed using multiple time scale integration techniques also developed by the principle authors. Nuclear quantum effects can be studied as well using the principle authors' path integral molecular dynamics methodology. Path integrals can be performed for both force-field based and ab initio calculations. Geometries such as surfaces, clusters and wires can also be studied using recently developed rigorous techniques by the principle authors.

The code is written in ``object-oriented'' styled C, which tightly couples data to functions. A migration to a truly object-oriented language such as C++ or a Java/C++ combination is planned for the near future. The code currently runs in a wide variety of serial, vector and parallel platforms. Parallel communication is handled via the MPI library. In addition, PINY_MD(c) contains a number of analysis tools to study electronic properties, calculate spectra, analyze structure in real and reciprocal spaces (e.g. neutron scattering partial structure factors).

New version available!!

Download the code (Aug. 30, 2005 version)

Download the pseudopotential library (October, 2005 version)

Download examples

Download additional new examples

These examples illustrate CP and path-integral CP for the HF Dimer

PINY_MD(c) Manual in PDF format

The following links with specific details about the code will soon be activated:

Dynamical generation of statistical ensembles.

Classical multiple time scale molecular dynamics.

Path integral molecular dynamics.

Ab initio molecular dynamics.

The bio-builder.

Analysis tools.

Code structure and design strategy.

The following is an (incomplete) list of publications based on the code:

Reaction Pathway of the [4+2] Diels-Alder adduct formation on Si(100)-2x1 P. Minary and M. E. Tuckerman, J. Am. Chem. Soc. 126, 13920 (2004)

A simple quantum mechanical/molecular mechanical (QM/MM) model for methanol J. A. Morrone and M. E. Tuckerman, Chem. Phys. Lett. 370, 406 (2003)

Molecular dynamics study of the connection between flap closing and binding of fullerene-based inhibitors of the HIV-1 protease Z. Zhu, D. I. Schuster and M. E. Tuckerman, Biochem. (in press)

Protonic defect in hydrogen-bonded liquids: Structure and dynamics in ammonia and comparison with water Y. Liu and M. E. Tuckerman, J. Phys. Chem. B 105, 6598 (2001).

Constant pressure path integral molecular dynamics studies of quantum effects in the liquid state properties of n-alkanes, E. Balog, A. L. Hughes, and G. J. Martyna, J. Chem. Phys. 112 870-880 (2000).

Simulation studies of liquid ammonia by classical ab initio, classical, and path-integral molecular dynamics, M. Diraison, M. E. Tuckerman and G. J. Martyna, J. Chem. Phys. 111 1906-1113 (1999).

Computer simulation studies of finite temperature conformational equilibrium in alanine-based peptides, S. Samuelson and G. J. Martyna, J. Phys. Chem. B 103 1752-1766 (1999).

A Molecular dynamics simulation of the HIV-1 protease complexes with C60 and fullerene-based anti-viral agents, H. Mi, M. E. Tuckerman, D. I. Schuster and S. R. Wilson, Electrochem. Soc. Proc. 99, 256 (1999).

Solvent, force field, temperature and quantum effects on the folding free energy surface of blocked alanine tripeptide, S. Samuelson, A. Hughes and G. J. Martyna, J. Chim. Phys., 94, 1503 (1997).

Methods and algorithms used in the code can be found in the following papers:

Reversible multiple time scale molecular dynamics, M. E. Tuckerman, G. J. Martyna and B. J. Berne, J. Chem. Phys. 97, 1990 (1992).

Nose-Hoover chains: The canonical ensemble via continuous dynamics, G. J. Martyna, M. E. Tuckerman and M. L. Klein, J. Chem. Phys. 97, 2635 (1992).

Efficient molecular dynamics and hybrid monte carlo algorithms for path integrals, M. E. Tuckerman, G. J. Martyna, M. L. Klein and B. J. Berne, J. Chem. Phys. 99, 2796 (1993).

Integrating the Car-Parrinello Equations I/II, M. E. Tuckerman and M. Parrinello, J. Chem. Phys. 100, 1302 (1994).

Integrating the Car-Parrinello Equations III, J. Hutter, M. E. Tuckerman and M. Parrinello, J. Chem. Phys. 102, 859 (1995).

Explicit reversible integration algorithms for extended systems methods, G. J. Martyna, M. E. Tuckerman, D. J. Tobias and M. L. Klein, Mol. Phys. 87, 1117 (1996).

Adiabatic path integral molecular dynamics methods .2. Algorithms J. Cao and G. J. Martyna, J. Chem. Phys. 104, 2028 (1996).

Two dimensional umbrella sampling techniques for the computer simulation study of helical peptides at thermal equilibrium: The 3K(I) peptide in vacuo and solution, S. Samuelson and G. J. Martyna, J. Chem. Phys. 109, 11061 (1998).

A new reciprocal space based method for treating long range forces in clusters, G. J. Martyna and M. E. Tuckerman, J. Chem. Phys. 110, 2810 (1999).

Molecular dynamics algorithm for path integrals at constant pressure, M. E. Tuckerman, A. L. Hughes and M. E. Tuckerman, J. Chem. Phys. 110, 3275 (1999).

Generalized moment thermostatting: a new continuous dynamical approach to the canonical ensemble, Y. Liu and M. E. Tuckerman, J. Chem. Phys. 112, 1685 (2000).

Understanding modern molecular dynamics methods, M. E. Tuckerman and G. J. Martyna, J. Phys. Chem. B 104, 159 (2000).

Exploiting multiple levels of parallelism in Molecular Dynamics based calculations via modern techniques and software paradigms,M. E. Tuckerman, D. A. Yarne, S. O. Samuelson, A. L. Hughes and G. J. Martyna, Comp. Phys. Comm., 128 333 (2000).

A dual length scale method for plane-wave based simulation studies of chemical systems modeled using mixed ab initio/empirical force field descriptions, D. A. Yarne, M. E. Tuckerman, and G. J. Martyna, J. Chem. Phys., 115, 3531 (2001).

A new reciprocal space based treatment of long range interactions on surfaces, P. Minary, M. E. Tuckerman, K. Pihakari, and G. J. Martyna, J. Chem. Phys. (in press).

On the use of the adiabatic molecular dynamics technique in the calculation of free energy profiles, L. Rosso, P. Minary, Z. Zhu, and M. E. Tuckerman, J. Chem. Phys.116, 4389 (2002)

Using novel variable transformations to enhance conformational sampling in molecular dynamics, Z. Zhu, M. E. Tuckerman, S. O. Samuelson and G. J. Martyna Phys. Rev. Lett. 88, 100201 (2002).

Algorithms and novel applications based on the isokinetic ensemble. I. Biophysical and path integral molecular dynamics, P. Minary, G. J. Martyna and M. E. Tuckerman, J. Chem. Phys. (in press)

Algorithms and novel applications based on the isokinetic ensemble. II. Ab initio molecular dynamics, P. Minary, G. J. Martyna and M. E. Tuckerman, J. Chem. Phys. (in press)

Acknowledgement: M.E.T. and D.A.Y. would like to thank Michael L. Klein for postdoctoral and graduate support, respectively, during the evolution of this software project.

As noted above, this page is continually under construction.

Mail comments and suggestions to:

mark.tuckerman@nyu.edu

This page is maintained by Profs. Mark E. Tuckerman (NYU) and Glenn J. Martyna. Support from NSF NSF CHE-0310107 NSF CHE-0121375, NSF CHE-0420870 and NSF CHE-0704036 is acknowledged.

Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.