Molecular Dynamic Simulation of united atom liquid n-hexane

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
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