Team:EPF-Lausanne/Theory

From 2009.igem.org

(Difference between revisions)
(New page: ==Molecular dynamics theory== Molecular dynamics simulation consists of the numerical, step-by-step, solution of the classical equations of motion. For this purpose we need to be able to ...)
 
(45 intermediate revisions not shown)
Line 1: Line 1:
-
==Molecular dynamics theory==
+
{{EPF-Lausanne09}}
 +
<div CLASS="epfltrick">__TOC__
 +
</div><div CLASS="epfl09">
 +
 
 +
 
 +
 
 +
<html><center>
 +
<font size="6" color="#007CBC"><i>Molecular dynamics theory</i></font>
 +
</center></html>
 +
<br>
 +
----
 +
<br>
Molecular dynamics simulation consists of the numerical, step-by-step, solution of the classical equations of motion. For this purpose we need to be able to calculate the forces acting on the atoms, and these are usually derived from a potential energy. This potential energy can be divided into:
Molecular dynamics simulation consists of the numerical, step-by-step, solution of the classical equations of motion. For this purpose we need to be able to calculate the forces acting on the atoms, and these are usually derived from a potential energy. This potential energy can be divided into:
-
* '''the non-bonded interactions''':   
+
==the non-bonded interactions:==  
-
**The ''Lennard-Jones potential'' is the most commonly used form, with two parameters: σ, the diameter, and ε, the well depth. It takes into account the Van der Waals forces. It represents the non-bonded forces and the total potential energy can be calculated from the sum of energy contributions between pairs of atoms. [[Image:lennard_jones_vdw_forces.jpg|frame|center|Lennard Jones potential ]]
+
*The ''Lennard-Jones potential'' is the most commonly used form, with two parameters: σ, the diameter, and ε, the well depth. It takes into account the Van der Waals forces. It represents the non-bonded forces and the total potential energy can be calculated from the sum of energy contributions between pairs of atoms.  
-
**when electrostatic charges are present, we add the ''Coulomb force'', where Q1, Q2 are the  charges and ϵ0 is the permittivity of free space
+
<center>
-
[[Image:Coulomb.jpg‎|200px|thumb|center|Coulomb force ]]
+
[[Image:lennard_jones_vdw_forces.jpg]] [[Image:Lennard_jones.jpg|300px|center|thumb|Lennard-Jones pair potential showing the r<sup>−12</sup> and r<sup>−6</sup> contributions]]
 +
</center>
 +
*when electrostatic charges are present, we add the ''Coulomb force'', where Q1, Q2 are the  charges and ϵ0 is the permittivity of free space
 +
[[Image:Coulomb.jpg‎|200px|center]]
-
* '''the bonded interactions''': angles, bonds and dihedral angles have to be taken into account
+
==the bonded interactions:==
-
[[Image:bonded.jpg‎|400px|thumb|center|Bonded forces ]]
+
Angles, bonds and dihedral angles have to be taken into account
 +
[[Image:bonded.jpg‎|400px|center]]
-
Too understand a bit more, you can see the following article:
+
To understand a bit more, you can see the following article:
[[Media:Introduction_to_molecular_Dynamics_Simulation.pdf‎ | Introduction to Molecular Dynamics Simulation - Michael P. Allen]]
[[Media:Introduction_to_molecular_Dynamics_Simulation.pdf‎ | Introduction to Molecular Dynamics Simulation - Michael P. Allen]]
 +
 +
 +
 +
<html>
 +
<p align="center" class="style1"><a href="#top"><img src="https://static.igem.org/mediawiki/2009/thumb/0/06/Up_arrow.png/50px-Up_arrow.png" alt="Back to top" border="0"></a><br></p>
 +
</html>
 +
<br>
 +
 +
</div><div CLASS="epfl09bouchon"></div>

Latest revision as of 12:23, 8 September 2009

Contents


Molecular dynamics theory



Molecular dynamics simulation consists of the numerical, step-by-step, solution of the classical equations of motion. For this purpose we need to be able to calculate the forces acting on the atoms, and these are usually derived from a potential energy. This potential energy can be divided into:

the non-bonded interactions:

  • The Lennard-Jones potential is the most commonly used form, with two parameters: σ, the diameter, and ε, the well depth. It takes into account the Van der Waals forces. It represents the non-bonded forces and the total potential energy can be calculated from the sum of energy contributions between pairs of atoms.
Lennard jones vdw forces.jpg
Lennard-Jones pair potential showing the r−12 and r−6 contributions
  • when electrostatic charges are present, we add the Coulomb force, where Q1, Q2 are the charges and ϵ0 is the permittivity of free space
Coulomb.jpg

the bonded interactions:

Angles, bonds and dihedral angles have to be taken into account

Bonded.jpg


To understand a bit more, you can see the following article: Introduction to Molecular Dynamics Simulation - Michael P. Allen


Back to top