Talk:Comparison of software for molecular mechanics modeling

Reference sections

Latest comment: 16 years ago3 comments3 people in discussion

Would it not be a good idea to add some references, e.g. for the algorithm details, e.g. for comparing force-fields, homology model algorithms, and semiempiric details? JKW (talk) 22:20, 11 November 2008 (UTC)Reply

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? --Bduke (Discussion) 01:55, 12 November 2008 (UTC)Reply

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: 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. --Thorwald (talk) 04:28, 12 November 2008 (UTC)Reply

Extended list

Latest comment: 16 years ago1 comment1 person in discussion

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:--Thorwald (talk) 21:35, 3 April 2009 (UTC)Reply

• ABINIT (DFT)
• 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)
• DL_POLY (classical)
• ESPResSo (classical, coarse-grained, parallel, extensible)
• Fireball (tight-binding DFT)
• GROMACS (classical)
• GROMOS (classical)
• GULP (classical)
• Hippo (classical)
• LAMMPS (classical, large-scale with spatial-decomposition of simulation ___domain for parallelism)
• 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)
• ProtoMol (classical, extensible, includes multigrid electrostatics)
• PWscf (DFT)
• S/PHI/nX (DFT)
• SIESTA (DFT)
• VASP (DFT)
• TINKER (classical)
• YASARA (classical)
• ORAC (classical)
• XMD (classical)