Talk:Molecular dynamics

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[edit] Article is too centered on biomolecules

OK, so I keep adding things about biomolecules because that's what I model. But I would ask people working in other fields with MD (i.e. metals) to add examples of applications. Jorgenumata 21:42, 22 October 2006 (UTC)

Hi Jorgenumata. I liked all the additions you have made. I myself have worked in metals on the physics side, so I can add some things. But actually, for the overall structure, I think it would be useful to discuss some of the ways that MD is used in different fields on the talk page so that we can incorporate the different uses of MD more fully. Most people are focused on their on field, and don't see outside it (me included), so it is kind of hard to incorporate all the different things into one article.
The merge discussion with MM is an example. Metals cannot be modelled by force fields. They are completely incompatible with the force field view of molecules, and from reading the MM page, MM only uses force fields. So it seems impossible to merge the articles. Anyway, enoough of my blabbing. The things that I am interested in knowing are what/how MD is used in different fields.
Fluid/aerodynamics: Do fluid dynamics / aerodynamics people use the billiard-ball approximation of atoms to model fluids, and are these methods considered molecular dynamics if they consider each atom individually?
Metals: We don't use force fields. Generally, TBSMA or equivalent is the least accurate/most empirical that can be used. Tight-binding and ab initio are far more common. Anyway, I can add a lot of metals things myself, so don't need much input here.
Semiconductors: Again, force fields are not used. However, requires very different approximations to metal simulations. Again, I can add stuff to the article on these.
Chemists: What exactly do chemists study? Are the chemical reactions always studied within a solvent, or are they studied on isolated chemical compounds? Is it always important to correctly model the temperature and pressure, or are these secondary considerations in chemical MD simulations?
Bio: Similar to chemistry, are temperature and pressure important? Do proteins get modelled within the context of a solvent, or are conformations studied on the basis of a single protein molecule with no external interactions?
So, I'll try to add some metals and semiconductor things to the article, but I don't want to break the chem/bio side. Will come back in maybe a week and try to do some additions. Mattopia 09:09, 21 November 2006 (UTC)

[edit] Merging of article Molecular Mechanics

I think the article on molecular mechanics is redundant and should be merged into this one, as well as some parts into force field (chemistry). It is completely equivalent, even from the content. The term "molecular dynamics" is nowadays more common than "molecular mechanics", except for the fixed expression QM/MM (quantum mechanics/molecular mechanics). What do you think? Jorgenumata 21:22, 9 October 2006 (UTC)

I disagree. The term is widely used in chemistry and molecular biology where the main thrust is to predict the equilibrium geometry. This is not dynamics. --Bduke 21:01, 10 October 2006 (UTC)

To expand on this, if you look at "Computational Chemistry" by David Young, "Essentials of Computational Chemistry" by Christopher Cramer and "Molecular Modelling" by Andrew Leach, you will find the two topics dealt with in different chapters. These are three of the key texts in computational chemistry. --Bduke 06:00, 11 October 2006 (UTC)

I agree with Bduke. MM is certainly much more narrowly focussed, than MD, on molecular geometry, especially to chemists. I do not agree that it should be merged with MD. vgsbox 23:58, 10 Oct. 2006

Also see Talk:Molecular_mechanics for more opinions... Itub 01:14, 15 October 2006 (UTC)

[edit] Force Fields

I added some stuff from a physics point of view, but I do struggle a bit with some of the terms used by chemists. In particular, what exactly is a force field? My supervisor used to say that what the protein-folders called a 'force field' was the same as what physicists called 'tight binding', but on reading the articles on force fields, that doesn't seem correct. Can anyone help ? Mattopia 07:32, 28 October 2005 (UTC)

Please see the distinction between force field (physics) and force field (chemistry). Karol 12:20, 28 October 2005 (UTC)

A succinct way to put it is that the force field specifies the form of the Hamiltonian for a classical system. As the force field (chemistry) article describes in some detail, most classical forcefields assume the dominant terms of their Hamiltonian to be some form of Van Der Waals force and some sort of coulombic electrostatic force and then one must come up with a set of VdW coefficients and partial charges deemed to be accurate enough for the problems of interest. There's some other spinach too but that's the main ideaRobotkid 12:06, 2 August 2006 (UTC)

[edit] Definition of MD

This article is misleading! The term "molecular dynamics" means simply the motion of molecules, such as translation, rotation, vibration, etc. Experimentally molecular dynamics can be probed by spectroscopy (Infra-Red, Microwave, Raman, etc.) and scattering etc. Molecular dynamics simulation is a computer simulation method that has been developed to understand the measured spectra and mainly to gain a deeper understanding of the motion of molecules. It aims to mimic the motion of molecules and atoms, and it aims to be consistent with spectroscopy. In theoretical circles, however, it is true that molecular dynamics refers usually to the simulation method, but that is not necessarily true among experimentalists. Galileo fan 10:29, 7 December 2005 (UTC)

I disagree - taken individually both the words "molecular" and "dynamics" are incredibly vague - even among experimentalists the use of such imprecise language becomes a problem because of the huge disparity in length-scales and time-scales between different experimental techniques (in NMR spectroscopy alone, "dynamics" can be measured from the picoseconds to the millisecond range). In terms of simulation, however, it refers to a very specific method of sampling via the integration of equations of motion which is not necessarily motivated by a need to reproduce spectroscopic data. In principle, any equilibrium property can be measured with molecular dynamics as a sampling technique (for example diffusion coefficients, osmotic/activity coefficients, dielectric constants). Robotkid 12:06, 2 August 2006 (UTC)

Molecular dynamics is quite a generic term. I suggest to split this article. Galileo fan is right. What it is in the current article must be classified as "Molecular Dynamics Simulation Methods, Techniques and Algorithms" Please let me know your ideas. Otherwise I will split the article.

Also subsection "Types of MD Systems" is not mathching with the sub-sections. "Force fields" or "inter-atomic potentials" is not a type of MD systems, simply they are the part of the technique.

--mcyp 09:00, 10 August 2006 (UTC)

[edit] Statistical Ensembles

I have edited some part. Pointing out integrators and their use in the corresponding Statistical Ensembles. Also, added senteces that corresponding Mathematical field on "Molecular Dynamics". There was an error that MD gives time dependent properties. That is a misconception. Equilibrium MD only gives static properties (time-independent or steady-state) where it is also based on Ergodic theory. Cheers

--mcyp 12:28, 2 August 2006 (UTC)

Hi Msuzen, I was wondering if you could move some of your additions into a sub-section on statistical mechanics and equilibrium/non-equilibrium systems in MD. When I first read your changes it took a little while to understand what you were saying, and I think it could do with more explanation. Unfortunately, I don't think I have the necessary knowledge to do it myself. Mattopia 15:14, 2 August 2006 (UTC)

Hello Mattopia, If you refer to having a new sub-section, it is a good idea. May we can add "Ensembles and Integrator Algorithms" and "Non-Equilibrium MD" sections? Any ideas?

--mcyp 08:43, 10 August 2006 (UTC)

it is the Gibbs hypothesis that time average equals the ensemble average

[edit] Torsion angle dynamics

I guess it is important to say something about torsion angle dynamics applied in DYANA and IVM module of XPLOR. Biophys 17:45, 31 October 2006 (UTC)

[edit] General to-dos

Posting here for wider reference.

  • Lead needs major work
  • General organization is awkward; algorithms section is ridiculously stubby
  • Rather little discussion of the implicit/explicit solvent decision
  • Barely anything on constraints??
  • Not terribly important, but grand canonical ensemble is missing
  • Problems of current force fields not covered/glossed over; should get a brief mention
  • Numerical issues not covered or barely covered - energy drift not even a brief mention? integration schemes? (only verlet gets even a link) and timesteps barely even get a sentence
  • PBC issues should be covered, though maybe best split into a subarticle (which is totally missing at the moment)

Opabinia regalis 04:10, 27 January 2007 (UTC)

[edit] Integrators

The integrator section needs to be redone. It contains several errors.

First of all, the Nose-Hoover temperature control is not an integrator; it's just a thermostat which gives some additional differential equations which control the system temperature. One still needs some algorithm to solve the equations. Same goes for Parinello-Rahman pressure control. These do not belong to the integrator section. In fact I'm going to remove them after this post.

Secondly, it's wrong to say that Verlet integrator is somehow microcanonical. There's no reason why one couldn't use some temperature/pressure control with it. Ossi 13:20, 8 May 2007 (UTC)

[edit] Large animation

Isn't the >600K animation a bit big to be in an article? Remember, some people are still on dial-up. 210.50.115.191 02:48, 24 September 2007 (UTC)

[edit] Ab-Initio Section Highly Illegible

This section needs work on general grammar and style and readability. 23:37, 4 October 2007 (UTC)

Add a tag? Pedro Gonnet 08:26, 5 October 2007 (UTC)
I just reworked and reorganized the ab-initio section. Still, we need an expert on this to tend to it. Jorgenumata 09:06, 8 October 2007 (UTC)

[edit] Databases of trajectories relevant to topic

These links to databases of molecular trajectories have been deleted twice. I think they are perfectly relevant to the topic of molecular dynamics. Jorgenumata 16:12, 31 October 2007 (UTC)

  • Dynameomics.org: Home page of the Dynameomics project and database of molecular dynamics simulations for several hundred folds
  • BioSimGrid, a database for biomolecular simulations
  • MolMovDB: A database of molecular motions
I'm the one who removed them. To my understanding, this article is more about molecular dynamics in general, which these links are not. There are more specific pages, such as Protein folding, Molecular mechanics, Molecular Modelling Protein structure prediction, Software for molecular mechanics modeling, List of protein structure prediction software, etc... where these links would be more at home.
Cheers, pedro gonnet - talk - 01.11.2007 08:10
Hola Pedro. Do you mean that this page should only be about the technical aspects of simulation, and not about the results, application and analysis? I think these links are useful for the readers to understand what you can do with MD. All the wikipedia entries you mentioned deal mainly with static concepts of proteins. These external links offer dynamic trajectories, which are the product of molecular dynamics simulations. Jorgenumata 13:18, 4 November 2007 (UTC)
Sorry for answering kind of late -- I'm out sick... I agree that Molecular trajectories are important enough and I guess the best thing to do would be to start a specific article on that topic and link it in the "See also" section of this and related articles. That way we resolve the problem of where things go and have all the relevant links on this topic. What do you think? Cheers, pedro gonnet - talk - 06.11.2007 11:01
Hola. Honestly I don't think molecular trajectories deserve a separate page. They are the sole product and objective of a molecular dynamics simulation, which is then to be analyzed. 160.45.24.162 (talk) 09:40, 20 November 2007 (UTC)