Биологический проект Налаштування

[Alien]

Как насчет сделать клиенты для громакса\намда с практическим применением в НИИ академии наук Украины?

[Death]

а как нащот http://en.wikipedia.org/wiki/CHARMM

http://en.wikipedia.org/wiki/AMBER

или ваще

http://en.wikipedia.org/wiki/List_of_softw...hanics_modeling

Major software for MD simulations

Main article: List of software for molecular mechanics modeling
Abalone (classical, implicit water)
ABINIT (DFT)
ACEMD (running on NVIDIA GPUs: heavily optimized with CUDA)
ADUN (classical, P2P database for simulations)
AMBER (classical)
Ascalaph (classical, GPU accelerated)
CASTEP (DFT)
CPMD (DFT)
CP2K (DFT)
CHARMM (classical, the pioneer in MD simulation, extensive analysis tools)
COSMOS (classical and hybrid QM/MM, quantum-mechanical atomic charges with BPT)
Desmond (classical, parallelization with up to thousands of CPU's)
Culgi (classical, OPLS-AA, Dreiding, Nerd, and TraPPE-UA force fields)
DL_POLY (classical)
ESPResSo (classical, coarse-grained, parallel, extensible)
Fireball (tight-binding DFT)
GROMACS (classical)
GROMOS (classical)
GULP (classical)
Hippo (classical)
Kalypso MD simulation of atomic collisions in solids
LAMMPS (classical, large-scale with spatial-decomposition of simulation domain for parallelism)
LPMD Las Palmeras Molecular Dynamics: flexible an modular MD.
MacroModel (classical)
MDynaMix (classical, parallel)
MOLDY (classical, parallel) latest release
Materials Studio (Forcite MD using COMPASS, Dreiding, Universal, cvff and pcff forcefields in serial or parallel, QMERA (QM+MD), ONESTEP (DFT), etc.)
MOSCITO (classical)
NAMD (classical, parallelization with up to thousands of CPU's)
NEWTON-X (ab initio, surface-hopping dynamics)
ORAC (classical)
ProtoMol (classical, extensible, includes multigrid electrostatics)
PWscf (DFT)
RedMD (coarse-grained simulations package on GNU licence)
S/PHI/nX (DFT)
SIESTA (DFT)
VASP (DFT)
TINKER (classical)
YASARA (classical)
XMD (classical)
[edit]Related software

VMD - MD simulation trajectories can be visualized and analyzed.
PyMol - Molecular Visualization software written in python
Packmol Package for building starting configurations for MD in an automated fashion
Sirius - Molecular modeling, analysis and visualization of MD trajectories
esra - Lightweight molecular modeling and analysis library (Java/Jython/Mathematica).
Molecular Workbench - Interactive molecular dynamics simulations on your desktop
BOSS - MC in OPLS
[edit]Specialized hardware for MD simulations

Anton - A specialized, massively parallel supercomputer designed to execute MD simulations.
MDGRAPE - A special purpose system built for molecular dynamics simulations, especially protein structure prediction.

вобщам главный вопрос как распараллелить большую задачу. у фолдинга это получается. а какой софт будет у боинковских клиентов уже неважно. хоть http://en.wikipedia.org/wiki/Molecular_modeling_on_GPU