Molecular Dynamic Simulation of united atom liquid n-hexane

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THEORETICAL PHYSICAL CHEMISTRY TU DARMSTADT 1. Aims The following practical deals with a MD simulation of liquid n-hexane by means of the simulation package YASP. During the practice, you will learn how to create a topology file for n-hexane which requires more information than that of water. You will study the torsion angle distribution as well as the internal molecular dynamics related to torsion by comparing the simulation carried out with two different torsion potential. Your tasks are the following: − Build the topology file, − Equilibrate the system, − Analyze the sampling of the system in equilibrium trajectory. 2. Building topology file The System In this exercise you will use a particular model of n-hexane (fig1). The carbon atoms together with the bound hydrogen atoms are gathered in a single super-atom named united atom, such that the molecule consists of six interaction centers of two species, four CH2 and two CH3 united atoms (fig2). This reduced number of degrees of freedom speeds up the simulation in contrast to a simulation where all the atoms are explicitly taken into account. You will use a relatively small system of 100 molecules. Fig1. n-hexane molecule. C6H14. Fig2. n-hexane molecule with in the united atom model. 2
THEORETICAL PHYSICAL CHEMISTRY TU DARMSTADT Topology file In the topology file, the following parameters should be used: • Atoms: CH3 CH2 Mass m 15 u 14 u LJ epsilon 0.73 kJ/mol 0.48 kJ/mol LJ sigma 0.3970 nm 0.3970 nm charge q 0 0 • Bonds: 0.153 nm • Angles:109.47 deg (tetrahedron angle!), 520 kJ/mol rad 2 • Torsions: Angle - [deg] Dihedral τ 0 Periodicity n K [kJ/mol] 180 1 9.8 180 2 6.6 180 3 10.6 1. the torsion potential has the following analytic shape 3 K n V ( τ ) = ∑ [ 1− cos( n( τ −τ 0 )) ] n= 1 2 2. Write the topology file for a single n-hexane molecule. Use the file hexane-1.tp (copy from directory /data/home/fleroy/students/exercises/prac4) as a starting point. It contains the keywords and information about the file format. 3. Create the system topology file hexane-100.tp with the tool jointp. Below is the topology file: title: hexane atoms: 6 1 'CH3' 15.0 0.73 0.397 0.000 2 'CH2' 14.0 0.48 0.397 0.000 3 'CH2' 14.0 0.48 0.397 0.000 4 'CH2' 14.0 0.48 0.397 0.000 5 'CH2' 14.0 0.48 0.397 0.000 6 'CH3' 15.0 0.73 0.397 0.000 constraints: 5 1 1 2 0.153 2 2 3 0.153 3 3 4 0.153 4 4 5 0.153 5 5 6 0.153 angles: 3
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Molecular Dynamic Simulation of united atom liquid n-hexane

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