ProtoMol- Molecular Dynamics Simulation / News: Recent posts

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.... read more

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
2.0.3):
* 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.... read more

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 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.

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.... read more

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

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

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.