Molecular Dynamic Simulation of united atom liquid n-hexane

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THEORETICAL PHYSICAL CHEMISTRY TU DARMSTADT 4 1 1 2 3 109.47 520.0 2 2 3 4 109.47 520.0 3 3 4 5 109.47 520.0 4 4 5 6 109.47 520.0 torsions: 9 1 1 2 3 4 180 1 9.8 2 1 2 3 4 180 2 6.6 3 1 2 3 4 180 3 10.6 4 2 3 4 5 180 1 9.8 5 2 3 4 5 180 2 6.6 6 2 3 4 5 180 3 10.6 7 3 4 5 6 180 1 9.8 8 3 4 5 6 180 2 6.6 9 3 4 5 6 180 3 10.6 modified_nonbonded: 12 1 1 2 0.0 0.0 0.0 0.0 2 1 3 0.0 0.0 0.0 0.0 3 1 4 0.8737 0.343 0.0 0.0 4 2 3 0.0 0.0 0.0 0.0 5 2 4 0.0 0.0 0.0 0.0 6 2 5 0.7843 0.3386 0.0 0.0 7 3 4 0.0 0.0 0.0 0.0 8 3 5 0.0 0.0 0.0 0.0 9 3 6 0.8737 0.343 0.0 0.0 10 4 5 0.0 0.0 0.0 0.0 11 4 6 0.0 0.0 0.0 0.0 12 5 6 0.0 0.0 0.0 0.0 molecules: 6 1 1 2 1 3 1 4 1 5 1 6 1 basta: 4
THEORETICAL PHYSICAL CHEMISTRY TU DARMSTADT 3. Molecular dynamics simulation NOTICE: Use mkmdinput to make an input file. For all the molecular dynamics here, cutoff is 1.1nm, neighbor list cutoff 1.2nm, verbose = 5. You may need copy files listed below from /data/students/exercises/prac4: hexane-1.tp, hexane-1.co, tor1.dat , tor2.dat, tor3.dat, merge.csh, average.cpp a. Create a box of equilibrated liquid n-hexane starting from a one molecule coordinate file The coordinate file hexane-1.co (copy from /data/home/fleroy/students/exercises/prac4) gives the coordinates of one n-hexane molecule. Now place 100 molecules into a box with the tool position. Before you run the program think about the box size. The molecules should not overlap, but the system should neither be too dilute. To obtain a reasonable box size for 100 n-hexane molecules, you can use density of liquid n-hexane at normal conditions to calculate it (656kg/mol, 298K). The calculated cubic box dimension along one direction is around 2.8nm. The system has to be equilibrated. This is done in two steps: in the first run the internal structure of the molecule should relax, so that strong deviations of internal degrees of freedom (e.g. angles) vanish, and overlaps of atoms are removed. In the second step the density has to be equilibrated. The system runs until the density has reached its final value. For equilibration, in our case, both NVT and NPT simulation are employed. 1). NVT: first, you should remove isotropic pressure coupling in the input file. Run the simulation 50000 steps with time-step (2fs) and temperature coupling time (300K, 0.2ps). 2). NPT: Now the density of the system has to be equilibrated using isotropic pressure control (101.3 0 1.0e-6 5). Start the simulation using the final output coordinates from the last simulation as the input coordinates. Another 50000 steps with the same time-step and the same temperature coupling time is run. 3). NPT: equilibrate the system again with NPT but with a shorter pressure coupling time (101.3 0 1.0e-6 2). Start the simulation using the final output coordinates from the last simulation as the input coordinates. Another 300000 steps (every 300 timestep is suggested for output) with the same timestep and the same temperature coupling time is run. 4). Monitor the density and temperature with plot_values, determing if it has equilibrated (exp. 656kg/mol, 298K). With the programs jmol or vmd, you can get an impression of the spatial structure of n-hexane. But before that, you need get a .xyz file using: yasp2xyz < md.co > md.xyz b. Production simulation Run a long simulation (about 100000 steps) using the final output coordinates from the last simulation as the input coordinates. Use the last input file, except changing the simulation steps (keep the other 5
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Molecular Dynamic Simulation of united atom liquid n-hexane

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