SklogWiki - User contributions [en]

Abalone

2009-04-24T18:46:02Z

Niki:

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

[http://www.agilemolecule.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]]

Abalone

2009-04-24T18:45:12Z

Niki:

[[Image:Abalone.png|300px|thumb| Protein simulation on Abalone]]

[http://www.agilemolecule.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]]

Materials modelling and computer simulation codes

2009-04-20T14:43:47Z

Niki:

The following is a sortable list (to change sort criteria click on the square icon next to the column title) of software for use in materials modelling and computer simulation.
{| class="wikitable sortable" border="1" cellpadding="5" cellspacing="0"
|-
! Computer program !! Focus !! class="unsortable" | Notes !! License
|-
|[[Abalone]]
|[[molecular dynamics]], visualisation
|biopolimers
|commercial
|-
|[[AMBER -- Assisted Model Building with Energy Refinement | AMBER]]
|[[molecular dynamics]]
|Assisted Model Building with Energy Refinement
|commercial
|-
|[[BOSS]]
|
| '''B'''iochemical and '''O'''rganic '''S'''imulation '''S'''ystem
|commercial
|-
|[[CASTEP]]
|[[density-functional theory]]
|
|commercial (free in United Kingdom)
|-
|[[CCP5 Program Library]]
|various
|program library
|free to academics
|-
|[[CHARMM]]
|
|'''C'''hemistry at '''HAR'''vard '''M'''olecular '''M'''echanics
|commercial
|-
|[[CPMD]]
|[[ab initio molecular dynamics]]
|'''C'''arr-'''P'''arrinello '''M'''olecular '''D'''ynamics
|free with [http://www.cpmd.org/cpmd_licence.html license]
|-
|[[Dalton]]
|
|Computational chemistry
|free with [http://www.theochem.kth.se/dalton/ license]
|-
|[[DiMol2D]]
|[[molecular dynamics]]
|Molecular dynamics visualization
|free executable
|-
|[[DL_MESO]]
|[[dissipative particle dynamics]]
|Mesoscale simulation package
|free source with [http://www.cse.scitech.ac.uk/ccg/software/DL_MESO/Registration.shtml academic license]
|-
|[[DL_POLY]]
|[[molecular dynamics]]
|Molecular simulation package
|free source with [http://www.cse.scitech.ac.uk/ccg/software/DL_POLY/Registration.shtml academic license]
|-
|[[ESPResSo]]
|[[molecular dynamics]]
|'''E'''xtensible '''S'''imulation '''P'''ackage for '''Res'''earch on '''So'''ft matter
|free
|-
|[[Etomica]]
|
|development environment
|free
|-
|[[Gaussian]]
|electronic structure
|Computational chemistry
|commercial
|-
|[[gdpc]]
|visualisation
|molecular dynamics visualisation
|free (GNU license)
|-
|[[GROMACS]]
|[[molecular dynamics]]
|
|free source
|-
|[[GROMOS]]
|[[molecular dynamics]]
|biomolecular systems
|free for academics, fee otherwise
|-
|[[HOOMD]]
|[[molecular dynamics]]
|'''H'''ighly '''O'''ptimized '''O'''bject Oriented '''M'''olecular '''D'''ynamics.
|free, Open Source
|-
|[[IMD]]
|[[molecular dynamics]]
|
|
|-
|[[LAMMPS]]
|[[molecular dynamics]]
|
|free source (GNU license)
|-
|[[MACSIMUS]]
|[[molecular dynamics]]
|'''MAC'''romolecule '''SIMU'''lation '''S'''oftware
|free
|-
|[[Materials Studio]]
|various
|
|commercial
|-
|[[MCCCS Towhee]]
|[[Monte Carlo]]
|
|free source
|-
|[[MCPRO]]
|[[Monte Carlo]]
|peptides, proteins, and nucleic acids in solution
|commercial
|-
|[[MDynaMix]]
|[[molecular dynamics]]
|molecular dynamics of mixtures
|free (GNU license)
|-
|[[Moldy]]
|[[molecular dynamics]]
|
|free
|-
|[[Molecular Workbench]]
|
|Interactive simulations
|free, Open Source
|-
|[[Moscito]]
|[[molecular dynamics]]
|
|free (General Public License)
|-
|[[Music]]
|
|'''Mu'''ltipurpose '''Si'''mulation '''C'''ode
|free (General Public License)
|-
|[[NAMD]]
|[[molecular dynamics]]
|
|free
|-
|[[NWChem]]
|
|Computational chemistry
|free
|-
|[[ORAC]]
|[[molecular dynamics]]
|
|free
|-
|[[PINY_MD]]
|[[molecular dynamics]]
|
|free
|-
|[[Protein Explorer]]
|visualisation
|molecular graphics
|free
|-
|[[RasMol]]
|visualisation
|molecular graphics
|free source
|-
|[[SIESTA]]
|[[ab initio molecular dynamics]]
|'''S'''panish '''I'''nitiative for '''E'''lectronic '''S'''imulations with '''T'''housands of '''A'''toms
|free for academics, fee otherwise
|-
|[[SYBYL]]
|various
|
|commercial
|-
|[[TINKER]]
|
|Software tools for molecular design
|free source
|-
|[[VASP]]
|[[Ab initio molecular dynamics]]
|
|
|-
|[[VMD]]
|visualisation
|Molecular dynamics visualisation in 3-dimensions
|free
|-
|[[WIEN2K]]
|
|Electronic structure calculation in solids
|commercial
|-
|[[XCrysDen]]
|visualisation
|Crystalline and molecular structure visualisation
|free (General Public License)
|-
|[[X-PLOR]]
|
|Computational structural biology
|
|-
|[[YASARA]]
|
|
|free & commercial
|-
|[http://www.theo.chemie.tu-darmstadt.de/group/services/yaspdoc/yaspdoc.html YASP]
|[[molecular dynamics]]
|
|
|}

[[category: Materials modelling and computer simulation codes]]

User:Niki

2009-04-18T22:04:49Z

Niki: New page: Hi. I am a chemist. Main interests: * Organic chemistry * Molecular modeling * Programs writing

Hi. I am a chemist. Main interests:
* Organic chemistry
* Molecular modeling
* Programs writing

User talk:Niki

2009-04-18T21:50:30Z

Niki: New page: Hi

SPC/F model of water

2009-04-18T21:33:28Z

Niki:

{{Stub-water}}
This model is a modified version of the simple point-charge model [[SPC]] for [[water]]. The SPC model is rigid,
whilst the '''SPC/F''' model is flexible. This model gives the correct density and dielectric permittivity of water. The model implemented in the programs [[MDynaMix]] and [[Abalone]].
==References==
#[http://dx.doi.org/10.1103/PhysRevB.31.2643 Kahled Toukan and Aneesur Rahman "Molecular-dynamics study of atomic motions in water", Physical Review B '''31''' pp. 2643 - 2648 (1985)]
[[category: water]]
[[category: models]]

Materials modelling and computer simulation codes

2009-04-18T13:16:42Z

Niki:

The following is a sortable list (to change sort criteria click on the square icon next to the column title) of software for use in materials modelling and computer simulation.
{| class="wikitable sortable" border="1" cellpadding="5" cellspacing="0"
|-
! Computer program !! Focus !! class="unsortable" | Notes !! License
|-
|[[Abalone]]
|[[molecular dynamics]], visualisation
|biopolimers
|commercial
|-
|[[AMBER -- Assisted Model Building with Energy Refinement | AMBER]]
|[[molecular dynamics]]
|Assisted Model Building with Energy Refinement
|commercial
|-
|[[BOSS]]
|
| '''B'''iochemical and '''O'''rganic '''S'''imulation '''S'''ystem
|commercial
|-
|[[CASTEP]]
|[[density-functional theory]]
|
|commercial (free in United Kingdom)
|-
|[[CCP5 Program Library]]
|various
|program library
|free to academics
|-
|[[CHARMM]]
|
|'''C'''hemistry at '''HAR'''vard '''M'''olecular '''M'''echanics
|commercial
|-
|[[CPMD]]
|[[ab initio molecular dynamics]]
|'''C'''arr-'''P'''arrinello '''M'''olecular '''D'''ynamics
|free with [http://www.cpmd.org/cpmd_licence.html license]
|-
|[[Dalton]]
|
|Computational chemistry
|free with [http://www.theochem.kth.se/dalton/ license]
|-
|[[DiMol2D]]
|[[molecular dynamics]]
|Molecular dynamics visualization
|free executable
|-
|[[DL_MESO]]
|[[dissipative particle dynamics]]
|Mesoscale simulation package
|free source with [http://www.cse.scitech.ac.uk/ccg/software/DL_MESO/Registration.shtml academic license]
|-
|[[DL_POLY]]
|[[molecular dynamics]]
|Molecular simulation package
|free source with [http://www.cse.scitech.ac.uk/ccg/software/DL_POLY/Registration.shtml academic license]
|-
|[[ESPResSo]]
|[[molecular dynamics]]
|'''E'''xtensible '''S'''imulation '''P'''ackage for '''Res'''earch on '''So'''ft matter
|free
|-
|[[Etomica]]
|
|development environment
|free
|-
|[[Gaussian]]
|electronic structure
|Computational chemistry
|commercial
|-
|[[gdpc]]
|visualisation
|molecular dynamics visualisation
|free (GNU license)
|-
|[[GROMACS]]
|[[molecular dynamics]]
|
|free source
|-
|[[GROMOS]]
|[[molecular dynamics]]
|biomolecular systems
|free for academics, fee otherwise
|-
|[[HOOMD]]
|[[molecular dynamics]]
|'''H'''ighly '''O'''ptimized '''O'''bject Oriented '''M'''olecular '''D'''ynamics.
|free, Open Source
|-
|[[IMD]]
|[[molecular dynamics]]
|
|
|-
|[[LAMMPS]]
|[[molecular dynamics]]
|
|free source (GNU license)
|-
|[[MACSIMUS]]
|[[molecular dynamics]]
|'''MAC'''romolecule '''SIMU'''lation '''S'''oftware
|free
|-
|[[Materials Studio]]
|various
|
|commercial
|-
|[[MCCCS Towhee]]
|[[Monte Carlo]]
|
|free source
|-
|[[MCPRO]]
|[[Monte Carlo]]
|peptides, proteins, and nucleic acids in solution
|commercial
|-
|[[MDynaMix]]
|[[molecular dynamics]]
|molecular dynamics of mixtures
|free (GNU license)
|-
|[[Moldy]]
|[[molecular dynamics]]
|
|free
|-
|[[Molecular Workbench]]
|
|Interactive simulations
|free, Open Source
|-
|[[Moscito]]
|[[molecular dynamics]]
|
|free (General Public License)
|-
|[[Music]]
|
|'''Mu'''ltipurpose '''Si'''mulation '''C'''ode
|free (General Public License)
|-
|[[NAMD]]
|[[molecular dynamics]]
|
|free
|-
|[[NWChem]]
|
|Computational chemistry
|free
|-
|[[ORAC]]
|[[molecular dynamics]]
|
|free
|-
|[[PINY_MD]]
|[[molecular dynamics]]
|
|free
|-
|[[Protein Explorer]]
|visualisation
|molecular graphics
|free
|-
|[[RasMol]]
|visualisation
|molecular graphics
|free source
|-
|[[SIESTA]]
|[[ab initio molecular dynamics]]
|'''S'''panish '''I'''nitiative for '''E'''lectronic '''S'''imulations with '''T'''housands of '''A'''toms
|free for academics, fee otherwise
|-
|[[SYBYL]]
|various
|
|commercial
|-
|[[TINKER]]
|
|Software tools for molecular design
|free source
|-
|[[VASP]]
|[[Ab initio molecular dynamics]]
|
|
|-
|[[VMD]]
|visualisation
|Molecular dynamics visualisation in 3-dimensions
|free
|-
|[[WIEN2K]]
|
|Electronic structure calculation in solids
|commercial
|-
|[[XCrysDen]]
|visualisation
|Crystalline and molecular structure visualisation
|free (General Public License)
|-
|[[X-PLOR]]
|
|Computational structural biology
|
|-
|[[YASARA]]
|
|
|free
|-
|[http://www.theo.chemie.tu-darmstadt.de/group/services/yaspdoc/yaspdoc.html YASP]
|[[molecular dynamics]]
|
|
|}

[[category: Materials modelling and computer simulation codes]]

Abalone

2009-04-17T23:17:01Z

Niki:

[[Image:Abalone.png|300px|thumb| Protein simulation on Abalone]]

[http://www.agilemolecule.com/Abalone/ 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]]

File:Abalone.png

2009-04-17T23:15:03Z

Niki: Protein simulation on Abalone

Protein simulation on Abalone

Abalone

2009-04-17T23:03:25Z

Niki:

[http://www.agilemolecule.com/Abalone/ 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]]

Abalone

2009-04-17T23:00:38Z

Niki: New page: [http://www.agilemolecule.com/Abalone/ Abalone] is a general purpose molecular dynamics and molecular graphics program for simulations of bio-molecules in a [[Boundary conditions |...

File:MeCN-simulation-on-MDynaMix.png

2009-04-17T22:35:04Z

Niki:

MDynaMix

2009-04-17T22:26:44Z

Niki:

[[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.agilemolecule.com/Ascalaph/Ascalaph_Designer.html Graphical shell for MDynaMix]

File:MeCN-simulation-on-MDynaMix-300.png

2009-04-17T22:12:11Z

Niki: MeCN box simulation on MDynaMix package.

MeCN box simulation on MDynaMix package.