Talk:Comparison of software for molecular mechanics modeling: Difference between revisions

Revision as of 17:54, 9 January 2009

Revision as of 21:35, 3 April 2009

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:Well each entry is linked to its own article, which presumably has references, or it it is linked to a reference. What else do you want? --[[User:Bduke|<span style="color:#002147;">'''Bduke'''</span>]] [[User_talk:Bduke|<span style="color:#002147;">'''(Discussion)'''</span>]] 01:55, 12 November 2008 (UTC)

::I think it is a good idea to always provide references (the original reference in, say, [[PubMed]]). This is because not every website makes it easy to find the associated references. I would suggest using an abbreviated form. Something like: [http://dx.doi.org/10.1016%2FS0263-7855%2898%2980030-1 Bacon D, ''et al.'', 1998] (for Raster3D and where the link is the DOI number). I also suggest we try to add all of the license types to each entry. --[[User:Thorwald|Thorwald]] ([[User talk:Thorwald|talk]]) 04:28, 12 November 2008 (UTC)

==Extended list==

The following list was taken from the [[Molecular dynamics#Major software for MD simulations]] section of that article. Some of these do not appear in this article and should be included:--[[User:Thorwald|Thorwald]] ([[User talk:Thorwald|talk]]) 21:35, 3 April 2009 (UTC)

* [[ABINIT]] (DFT)

* [http://cbbl.imim.es/Adun ADUN] (classical, P2P database for simulations)

* [[AMBER]] (classical)

* [http://www.agilemolecule.com/Products.html Ascalaph] (classical, [[GPU]] accelerated)

* [[CASTEP]] (DFT)

* [[CPMD]] (DFT)

* [http://cp2k.berlios.de/ CP2K] (DFT)

* [[CHARMM]] (classical, the pioneer in MD simulation, extensive analysis tools)

* [http://www.cosmos-software.de/ce_intro.html COSMOS] (classical and hybrid QM/MM, quantum-mechanical atomic charges with BPT)

* [http://www.DEShawResearch.com/resources.html Desmond] (classical, parallelization with up to thousands of CPU's)

* [http://www.ccp5.ac.uk/DL_POLY/ DL_POLY] (classical)

* [[ESPResSo]] (classical, coarse-grained, parallel, extensible)

* [http://fireball-dft.org Fireball] (tight-binding DFT)

* [[GROMACS]] (classical)

* [[GROMOS]] (classical)

* [[General Utility Lattice Program|GULP]] (classical)

* [http://www.biowerkzeug.com/ Hippo] (classical)

* [[LAMMPS]] (classical, large-scale with spatial-decomposition of simulation ___domain for parallelism)

* [[MDynaMix]] (classical, parallel)

* [http://www.ccp5.ac.uk/moldy/moldy.html MOLDY] (classical, parallel) [http://ccpforge.cse.rl.ac.uk/frs/?group_id=34 latest release]

* [http://accelrys.com/products/materials-studio/ 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)

* [http://www.univie.ac.at/newtonx/ NEWTON-X] (ab initio, surface-hopping dynamics)

* [http://protomol.sourceforge.net/ ProtoMol] (classical, extensible, includes multigrid electrostatics)

* [[PWscf]] (DFT)

* [http://www.sphinxlib.de S/PHI/nX] (DFT)

* [[SIESTA (computer program)|SIESTA]] (DFT)

* [[Vienna Ab-initio Simulation Package|VASP]] (DFT)

* [[TINKER]] (classical)

* [http://www.yasara.org YASARA] (classical)

* [http://www.chim.unifi.it/orac/ ORAC] (classical)

* [[XMD]] (classical)