We are pleased to announce the release of ProtoMol v2.0: a free, 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 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
- Novel integrators including Shadow Hyrid Monte Carlo (SHMC),
isothermal-isobaric MD, and isomolar-semigrand MD.
- 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, http://protomol.sourceforge.net,
where C++ source code, documentation, and prebuilt binaries may be found.
Operating systems natively supported include Linux, SunOS, Irix, HP-UX and
Windows.
We have also configured a new mailing list to better serve our user base.
Please visit the following link and join the list for support and development
news:
http://lists.sourceforge.net/lists/listinfo/protomol-users
Protomol user and development questions can be sent to the list using the
following email address:
[log in to unmask]
For questions or comments, please feel free to contact the ProtoMol team at
[log in to unmask]
To join or leave the molecular-dynamics-news email list, go to:
http://www.jiscmail.ac.uk/lists/molecular-dynamics-news.html
|