|
ProtoMol - DUMA: Development, User contact and MAintainance
ProtoMol
ProtoMol is an object-oriented component based framework for molecular
dynamics simulations. The framework supports the CHARMM 19 and 28a2 force
fields and is able to process PDB, PSF, XYZ and DCD trajectory files. It
is designed for high flexibility, easy extendibility and maintenance, and
high performance demands, including parallelization. The technique of
multiple time-stepping has been used to improve long-term efficiency, and
the use of fast electrostatic force evaluation algorithms like plain Ewald ,
Particle Mesh Ewald , and Multigrid summation further improves
performance. Longer time steps are possible using MOLLY, Langevin Molly
and Hybrid Monte Carlo , Nose-Hoover, and Langevin integrators. In
addition, ProtoMol has been designed to interact with VMD, a visualization
engine developed by the University of Illinois that is used for displaying
large biomolecular systems in three dimensions. ProtoMol is free
distributed software, and the source code will be included.
Features of ProtoMol
- An object-oriented component based framework for molecular dynamics simulations
- Designed for high flexibility, easy extendibility and maintenance, and high performance demands
- Incremental parallelization combining sequential and parallel environment
- Support of generic multiple time-stepping integration schemes
- Generic forces and potentials
- Fast electrostatic force evaluation algorithms:
- Ewald summation, O(N3/2)
- Particle-Mesh-Ewald, O(N log N)
- Multi-grid method, O(N)
- Support of common I/O formats (pre- & post-processing)
- 106 particle systems
ProtoMol is been developed in collaboration with J.A. Izaguirre and members of
the LCLS Group; CSE
Department, University of Notre Dame,
Indiana, USA.
ProtoMol is available at sourceforge.
Structural
BioCore/Biology Software Database: ProtoMol.
ProtoMol Tutorial (PDF)
Download
Source
& Binaries
Examples
Running ProtoMol
./protomol 3mg7ca.conf
In order to get help:./protoml -h
To figure out the supported forces:./protoml -f
To figure out all possible keywords:./protoml -k
Visualization
ProtoMol writes DCD files, which can be read by VMD.
Movies
- Movie of 50 Ca+40 + 50
A2+80 ions convering to a sphere (MPEG, 0.1ms, 13MB/MPEG, 1ms, 11MB/ ), 1000 frames, T. Matthey.
- Water 423 (MPEG) 9 MB, 500
frames, T.Matthey
- Movie of 41 Ca+ ions converging to a string (MPEG, 322KB), see also BER200.
- Movie of 42 Ca+ ions converging to a zig-zag line (MPEG, 320KB), see also BER200.
- 7 Spheres - Ugelstad spheres (MPEG) 7 MB, 1000 frames, A.Hellesøy.
- 7 Spheres - Ugelstad spheres with reflection (MPEG) 81 MB, 6000 frames,
A.Hellesøy.
- 7 Spheres - Ugelstad spheres (MOV - Round The World) 89 MB, A.Hellesøy.
- 7 Spheres - Ugelstad spheres (MOV- Sinatra) 84 MB, A.Hellesøy.
- The coalescence of two water droplets in a gas
phase, with surfactant molecules present. The model consists of
particles representing hydrophilic and hydrophobic groups interacting
via a modified Lennard Jones potential; MPEG
(27 MB/53 MB) 500/1000
frames, L.Rekvig
- Solar system (AVI -
The Universe Song) 86 MB, A.Hellesøy.
Documentation
- ProtoMol documentation.
- A Front End Design For Simulation Engines (PS) (PDF) (HTML) (Jesus A. Izaguirre with Trevor M. Cickovski).
- A Tutorial on the Prototyping of Multiple Time Stepping
Integrators for Molecular Dynamics (PS)
(PDF)(Jesus A. Izaguirre with Thierry Matthey, Jeremiah Willcock, Branden
Moore, Qun Ma, Thomas Slabach, George Viamontes), submitted to Proceedings of Methods for Macromolecular Modeling, in Lecture Notes in Computational Science and
Engineering, Springer-Verlag, 2001.
- ProtoMol Tutorial (PDF)
(T. Matthey), Nov. 2002.
- My ProtoMol research log, really technical!
User Groups
Related Links
TTP5 Presentation - Status Report
- Bergen 25/6 2001 (PDF)
- Tromsø 14/12 2001 (PDF)
- Oslo 11/06 2002 (PDF)
- Fevik 30/08 2002 (PDF)
- Trondheim 11/12 2002 (PDF)
Last modified: Friday, 23-Sep-2005 13:15:40 CEST.
|
