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Preview: Project News: ProtoMol- Molecular Dynamics Simulation

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Last Build Date: Thu, 28 May 2009 18:21:02 -0000


ProtoMol 3.0 released

Thu, 28 May 2009 18:21:02 -0000

The Laboratory for Computational Life Sciences at the University of Notre Dame is pleased to announce a new release of ProtoMol, version 3.0, now available for download on SourceForge. ProtoMol is an object-oriented framework for molecular dynamics simulations, designed for flexibility,
extensibility, and performance.
Key features added to ProtoMol 3.0 :
(1) Interface to OpenMM, an MD library with NVIDIA and ATI general purpose GPU support. OpenMM supports AMBER force fields and Generalized-Born implicit solvent.

(2) Python bindings offered as MDLab, which allow for prototyping of high level sampling protocols, new integrators, and new force calculations in Python.

(3) Coarse grained normal mode analysis (CNMA), which provides a scalable O(N^{9/5}) time and O(N^{3/2}) memory diagonalization. CNMA approximates low frequency modes very well.

(4) Normal Mode Langevin (NML) dynamics, which uses CNMA to periodically compute low frequency bases for propagation of dynamics, while fast modes are minimized to their equilibrium position. NML allows timesteps of 100 fs and more for even small proteins (> 30 residues) with real speedups that are about a third of the timestep used.

(5) Full checkpointing support, which simplifies use in distributed computing platforms such as Condor or Folding@Home.

ProtoMol 2.1 Released

Mon, 16 Jul 2007 12:38:55 -0000

The Laboratory for Computational Life Sciences at the University of
Notre Dame
is pleased to announce a new release of ProtoMol, version 2.1,
now available for download on SourceForge. ProtoMol is an object-oriented
framework for molecular dynamics simulations, designed for flexibility,
extensibility, and performance.

The following features have been added to the previous release (version
* Normal mode integrator and minimizer, along with mass reweighted
Hessian calculations and binary eigenvector file I/O.
* Conjugate gradient minimizer.
* Interfacing to Simtk LAPACK libraries for fast matrix operations.
* Improved Monte Carlo sampling with the Box/Mueller method for
random numbers.
* More control over Shadow Hybrid Monte Carlo, including
the ability to pause shadow computation along with customization
via timestep and the c value, which controls level of acceptance.
* Replica Exchange Method (REM) application.
* An implicit solvent model based on distance-dependent dielectric.
* Ability to compute dihedral Hessians.
* Continuous switching functions with user-specified order.
* Minimal image for all atom position output.
* Binary XYZ trajectory file output for positions and velocities.
* Several low-level optimizations.

Replica Exchange Available in CVS

Thu, 06 Apr 2006 17:26:51 -0000

The Replica Exchange Method (also called Parallel Tempering) has been implemented in ProtoMol using MPI for effecient communication. Their are also scripts in the tools directory to perform REM using ProtoMol over a heterogenous distributed system. The most current files are available via CVS.

Improved non-bonded force look up tables

Wed, 13 Jul 2005 09:08:18 -0000

Improved look up tables for non-bonded forces/potentials, e.g. Coulomb, LennardJones, Ewald real part and MultiGrid direct part. The approach uses a generic base class with policies to define the function/potential to be tabulated and with a given precision; suited for expesive potentials and swichting function, i.e., Ewald real part, LennardJones, C2. The default tabulated forces have relative force error of order 1e-6.

Protomol 2.0 Framework Released

Sat, 07 May 2005 15:41:06 -0000

We are pleased to announce the release of ProtoMol v2.0: an open source, object-oriented, component-based framework for molecular dynamics (MD) simulations. It supports CHARMM 19 and 28a2 force fields and is able to read and write PDB, PSF, XYZ, DCD, and several common graphics formats. ProtoMol is designed for high flexibility, ease of extendibility and maintenance, and high performance and scalability demands. We use MPI to implement atom- and force-based decompositions in a manner nearly transparent to both end-users and developers. The use of fast electrostatic force evaluation algorithms like particle mesh Ewald (PME), an O(n log n) method, and multigrid summation (MG), an O(n) method, further improve performance. In addition, MG has superior scalability when running in a parallel environment.

ProtoMol contains many novel MD and Monte Carlo (MC) based methods suitable for simulation in a variety of ensembles. For example, shadow hybrid Monte Carlo (SHMC) has been shown to scale with system size and MD timestep by a factor of 10 or more over hybrid Monte Carlo (HMC). Multiscale simulations may take advantage of longer timesteps by coupling multiple time-stepping algorithms with advanced integrators. Using targeted Molly, we have achieved stable timesteps of 16fs for solvated proteins. In addition, ProtoMol has been designed to interact with VMD, a visualization engine developed at the University of Illinois, which is used for displaying large biomolecular systems and running simulations in 3-D.

Highlights of ProtoMol v2.0:
- Average 50% performance increase versus ProtoMol 1.8.3
- Additional integrators including SHMC, an NPT method based upon the work of Maryna, Tobias, and Klein, and an MD implementation of the isomolar-semigrand ensemble for computing phase equilibrium of mixtures.
- An updated interface for adding new forces, integrators, and output methods
- Improved code organization utilizing design patterns

We invite you to visit the ProtoMol home page,, where C++ source code, documentation, and prebuilt binaries may be found. Operating systems natively supported include Linux, SunOS, Irix, HP-UX and Windows.

For questions or comments, please feel free to contact the ProtoMol team at

Windows compilation

Tue, 17 Feb 2004 15:35:22 -0000

All tools applications compile under Windows properly. Furthermore, a Windows release related bug was fixed.

Release 1.8.3

Fri, 23 Jan 2004 20:29:15 -0000

- enhanced load balancing
- parallel multigrid, Ewald and PME, incl. FFT
- binaries for AIX, IRIX, SUN, Linux, HP-UX and Windows

Transfer to SourceForge

Tue, 08 Jul 2003 18:30:35 -0000

We are in the process of moving ProtoMol to SourceForge, once the cvs/shell is ready for us to use, we will upload the old cvs directory for their support team to import it so we keep all of our history, and then we will be officially on SourceForge. If you need to be added to the Members Section of the ProtoMol SourceForge site please email the admin, mnyerges.