WikiNode

2012-07-02T15:02:18Z

193.232.68.75: /* Wiki neighbours */

This is the WikiNode page for '''SklogWiki'''. SklogWiki is a wiki for anyone interested in [[Classical thermodynamics | thermodynamics]], [[statistical mechanics]] and the [[Computer simulation techniques | computer simulation]] of materials, especially liquids and soft condensed matter. See [[Wikis and Science 2.0]] for more details about wikis, and [[SklogWiki:About]] for more information about this wiki.
==Wiki neighbours==
Here is an incomplete table of wikis that are dedicated to themes related to either the physical sciences, or to mathematics.
{| class="wikitable sortable" border="1" cellpadding="5" cellspacing="0"
|-
! class="unsortable" | Wiki name !!class="unsortable" | field !! class="unsortable" | notes !! | page count !! | [http://arxiv.org/abs/0902.3439 wikiFactor]
|-
|[[Main Page | SklogWiki]]
|[[statistical mechanics]], [[Classical thermodynamics |thermodynamics]]
|This wiki
| {{NUMBEROFARTICLES}}
|[[Special:PopularPages |20]]
|-
|[http://www.smac.lps.ens.fr/ SMAC-wiki]
|[[statistical mechanics]], [[Classical thermodynamics |thermodynamics]]
|dedicated to the book "Statistical Mechanics: Algorithms and Computations" by [http://www.lps.ens.fr/~krauth/ Werner Krauth]
|[http://www.smac.lps.ens.fr/index.php/Special:Statistics 111]
|[http://www.smac.lps.ens.fr/index.php/Special:Popularpages 6]
|-
|[http://www.gromacs.org/ GROMACS wiki]
|[[statistical mechanics]], [[Classical thermodynamics |thermodynamics]]
|deals with [[GROMACS]], a versatile package to perform [[molecular dynamics]]
|unknown
|[http://www.gromacs.org/Special:Popularpages 24]
|-
|[http://matdl.org/matdlwiki/index.php/Main_Page NSDL MatDL Pathway] including [http://matdl.org/matdlwiki/index.php/softmatter:Main_Page The Soft Matter Wiki]
|[[statistical mechanics]], [[Classical thermodynamics |thermodynamics]]
|(site apparently inactive)
|[http://matdl.org/matdlwiki/index.php/Special:Popularpages 22]
|[http://matdl.org/matdlwiki/index.php/Special:Popularpages 4]
|-
|[https://www.thermalfluidscentral.org/e-encyclopedia/index.php/Main_Page '''T'''hermal-'''F'''luids'''P'''edia]
|[[Classical thermodynamics |thermodynamics]]
|thermal and fluid science
|[https://www.thermalfluidscentral.org/e-encyclopedia/index.php/Special:Statistics 620]
|[https://www.thermalfluidscentral.org/e-encyclopedia/index.php/Special:PopularPages 10]
|-
|[http://www.cfd-online.com/Wiki/Main_Page CFD-Wiki]
|computational fluid dynamics
|
|[http://www.cfd-online.com/Wiki/Special:Statistics 465]
|[http://www.cfd-online.com/Wiki/Special:PopularPages 38]
|-
|[http://wiki.math.toronto.edu/DispersiveWiki/index.php/Main_Page Dispersive PDE Wiki]
|non-linear dispersive and wave equations
|
|[http://wiki.math.toronto.edu/DispersiveWiki/index.php/Special:Statistics 338]
|[http://wiki.math.toronto.edu/DispersiveWiki/index.php/Special:PopularPages 12]
|-
|[http://qwiki.stanford.edu/wiki/Main_Page Qwiki]
|quantum mechanics
|devoted to the collective creation of technical content for practising scientists. [http://qwiki.stanford.edu/wiki/Wikis (WikiNode)]
|[http://qwiki.stanford.edu/index.php/Special:Statistics 1676]
|[http://qwiki.stanford.edu/index.php/Special:PopularPages 24]
|-
|[http://www.quantiki.org/ Quantiki]
|quantum mechanics
| a free-content WWW resource in quantum information science
|[http://www.quantiki.org/wiki/Special:Statistics 222]
|[http://www.quantiki.org/wiki/index.php/Special:PopularPages 17]
|-
|[http://www.physics.thetangentbundle.net/wiki/Main_Page The Tangent Bundle]
|physics (general)
|a repository of ideas in physics
|[http://www.physics.thetangentbundle.net/wiki/Special:Statistics 644]
|[http://www.physics.thetangentbundle.net/wiki/Special:Popularpages 9]
|-
|[http://www.plasma-universe.com/index.php/Plasma-Universe.com Plasma-Universe.com]
|plasma
|to highlight the importance of plasma throughout the Universe
|[http://www.plasma-universe.com/Special:Statistics 87]
|[http://www.plasma-universe.com/index.php/Special:Popularpages 19]
|-
|[http://www.wikiwaves.org/Main_Page Wikiwaves]
|wave physics
|devoted to the mathematics of water waves
|[http://www.wikiwaves.org/Special:Statistics 362]
|[http://www.wikiwaves.org/Special:PopularPages 14]
|-
|[http://usefulchem.wikispaces.com/ UsefulChem]
|chemistry
|an open source science project in chemistry led by the Bradley Laboratory at Drexel University
|[http://usefulchem.wikispaces.com/space/pagelist 523]
|unknown
|-
|[http://www.ch.ic.ac.uk/wiki/index.php/Main_Page ChemWiki]
|chemistry
|Chemistry Department Wiki, Imperial College London (editing restricted to Imperial College users)
|[http://www.ch.ic.ac.uk/wiki/index.php/Special:Statistics 1901]
|[http://www.ch.ic.ac.uk/wiki/index.php/Special:Popularpages 11]
|-
|[http://chemwiki.ucdavis.edu/ ChemWiki]
|chemistry
|A free 'General Chemistry textbook' (Chemistry department at UC Davis)
| unknown
|[http://chemwiki.ucdavis.edu/Special:Popularpages 41]
|-
|[http://quixote.wikispot.org/Front_Page Quixote project]
|chemistry
|compilation of computational chemistry data
| unknown
| unknown
|-
|[http://nmrwiki.org NMRWiki]
|chemistry
|Magnetic Resonance-themed wiki (NMR,EPR,MRI). ([http://nmrwiki.org/wiki/index.php?title=Scientific_Wiki_Sites wikiNode])
|[http://nmrwiki.org/wiki/index.php?title=Special:Statistics 720]
|[http://nmrwiki.org/wiki/index.php?title=Special:Popularpages 14]
|-
|[http://www.mathematics.thetangentbundle.net/wiki/Main_Page The Tangent Bundle Mathematics Project]
|[[mathematics]]
|a repository of ideas in mathematics
|[http://www.mathematics.thetangentbundle.net/wiki/Special:Statistics 265]
|[http://www.mathematics.thetangentbundle.net/wiki/Special:Popularpages 6]
|-
|[http://www.maths.tcd.ie/~mathsoc/w/index.php?title=Main_Page mathsoc]
|[[mathematics]]
|Dublin University Mathematical Society
|[http://www.maths.tcd.ie/~mathsoc/wiki/Special:Statistics 136]
|[http://www.maths.tcd.ie/~mathsoc/wiki/Special:Popularpages 12]
|-
|[http://www.tricki.org/ Tricki]
|[[mathematics]]
|a repository of mathematical know-how
|unknown
|unknown
|-
|[http://groupprops.subwiki.org/wiki/Main_Page Groupprops]
|[[mathematics]]
|group theory wiki
|[http://groupprops.subwiki.org/wiki/Special:Statistics 5946]
|[http://groupprops.subwiki.org/wiki/Special:PopularPages 10]
|-
|[http://michaelnielsen.org/polymath1/index.php?title=Main_Page Polymath]
|[[mathematics]]
|collaborative online mathematical projects
|[http://michaelnielsen.org/polymath1/index.php?title=Special:Statistics 145]
|[http://michaelnielsen.org/polymath1/index.php?title=Special:PopularPages 14]
|-
|[http://www.scholarpedia.org/ Scholarpedia]
|[[mathematics]] (dynamical systems), physics
|Peer-reviewed open-access encyclopedia written by scholars from all around the world.
|[http://www.scholarpedia.org/article/Special:Statistics 2284]
|unknown
|-
|[http://www.proofwiki.org/wiki/Main_Page ProofWiki]
|[[mathematics]]
|Online compendium of mathematical proofs
|[http://www.proofwiki.org/wiki/Special:Statistics 5304]
|[http://www.proofwiki.org/wiki/Special:PopularPages 9]
|-
|[http://oeis.org/wiki/Main_Page OEIS Wiki]
|[[mathematics]]
|On-Line Encyclopedia of Integer Sequences
|[http://oeis.org/wiki/Special:Statistics 178433]
|[http://oeis.org/wiki/Special:PopularPages 5]
|-
|[http://plastics.inwiki.org/Main_Page Plastics Wiki]
|plastics
|an encyclopaedia of plastic materials. [http://plastics.inwiki.org/Plastics_Wiki:TourBusStop (TourBusStop)]
|[http://plastics.inwiki.org/Special:Statistics 1551]
|[http://plastics.inwiki.org/Special:Popularpages 20]
|-
|[http://www.layruoru.com/dokuwiki/doku.php/ Molecular modeling Wiki]
|molecular mechanics
|Some of the practices of molecular dynamics and Monte Carlo
|unknown
|unknown
|}

__NOTOC__
[[category: Miscellaneous]]

Abalone

2010-07-27T15:09:01Z

193.232.68.75:

[[Image:Abalone.png|thumb| Protein simulation on Abalone]]
[http://www.biomolecular-modeling.com/Abalone/index.html Abalone] is a [[molecular dynamics]], Hybrid [[Monte Carlo]] and molecular graphics program for simulations of bio-molecules in a [[Periodic boundary conditions |periodic rectangular cell]] in explicit water ([[SPC/F]]) or in implicit [[water models]]. Abalone is mainly designed to simulate [[proteins | protein]] folding and DNA-ligand complexes.
==References==
==External links==
*[http://www.biomolecular-modeling.com/ Agile Molecule]
[[Category: Materials modelling and computer simulation codes]]

MDynaMix

2010-01-21T13:04:07Z

193.232.68.75: /* External links */

[[Image:MeCN-simulation-on-MDynaMix-300.png|300px|thumb|MeCN box simulation on MDynaMix package]]

[http://www.fos.su.se/~sasha/mdynamix/ MDynaMix] (an acronym for '''M'''olecular '''Dyna'''mics of '''Mix'''tures) is a general purpose [[molecular dynamics]] code for simulations of [[mixtures]] of either rigid or [[flexible molecules]], interacting by a [[Force fields |force field]] consisting of [[Lennard-Jones model |Lennard-Jones]], electrostatic, covalent bonds, angles and torsion angles potentials as well as of some optional terms, in a [[Boundary conditions |periodic rectangular, hexagonal or truncated octahedron cell]]. Rigid bonds are constrained by the [[SHAKE]] algorithm. In case of flexible molecular models the [[double time step algorithm]] is used. Algorithms for [[Microcanonical ensemble |NVE]], [[Canonical ensemble |NVT]] and [[Isothermal-isobaric ensemble |NpT]] statistical [[Ensembles in thermostatistics |ensembles]] are implemented, as well as [[Ewald sum]] for treatment of the electrostatic interactions. Treatment of quantum correction to the atomic motion can be done within the [[Path integral formulation |path integral molecular dynamics]] approach. Package works on ''Unix/Linux'' workstations and clusters of workstations as well as on ''Windows'' in sequential mode.
==References==
#[http://dx.doi.org/10.1016/S0010-4655(99)00529-9 Alexander P. Lyubartsev and Aatto Laaksonen "M.DynaMix – a scalable portable parallel MD simulation package for arbitrary molecular mixtures", Computer Physics Communications '''128''' pp. 565-589 (2000)]
[[Category: Materials modelling and computer simulation codes]]

== External links ==
* [http://www.biomolecular-modeling.com/Ascalaph/Ascalaph_Designer.html Graphical shell for MDynaMix]

Abalone

2010-01-21T13:02:36Z

193.232.68.75:

[[Image:Abalone.png|thumb| Protein simulation on Abalone]]

[http://www.biomolecular-modeling.com/Abalone/index.html Abalone] is a general purpose [[molecular dynamics]] and [[molecular graphics]] program for simulations of bio-molecules in a [[Boundary conditions |periodic rectangular cell]] in explicit water ([[SPC/F]]) or in [[implicit water]] models. Mainly designed to simulate the [[proteins]] folding and DNA-ligand complexes.
[[Category: Materials modelling and computer simulation codes]]

SklogWiki - User contributions [en]

WikiNode

Abalone

MDynaMix

Abalone