Molecular Dynamic Simulation of united atom liquid n-hexane

THEORETICAL PHYSICAL CHEMISTRY TU DARMSTADT
parameters the same, every 50 timestep is suggested for output). Keep the final output file and
trajectory file as the source for data analysis.
4. Analysis of results
Now the production run can be analyzed. We will use some of the tools of YASP to analyze the
behavior of the conformations.
1. Compute the average mass density of the system.
Use plot_values tool.
2. Use the program trjtors and extract data file of torsion angles time-dependence.
trjtors trj_file < template_file
For this you need to specify a template file for each torsion. Use the files tor1.dat, tor2.dat, and
tor3.dat separately as template_file for dihedral angle 1, 2, and 3. You need to create a different
directory for each torsion. For example use directory /torsion1 (head torsion) for dihedral angle 1,
including the output trajectory file, and the template file (tor1.dat) there. Using the tool trjtors, you
will obtain 100 files that represent 100 molecules with two columns, indicating time and respective
torsional angle. The output files created by trjtors are automatically named as t00001,
t00002,…t00100.
3. Merge all the files into a resulting file using merge.csh that you will copy from
/data/home/fleroy/students/exercises/prac4
./merge.csh
After running merge.csh, you obtain a file named as resultfile that includes all torsional data for 100
molecules. Use it as input file for the program torsclass to sort torsional angles into conformations.
The torsional angles are divided into three states: gauch + (0-120degree), trans (120-240), gauch - (240-
360), set as 1, 2, 0 .
torsclass 120 240 360 < resultfile > tors_state
The output file “tors_state” contains two columns; one is the time the other is an integer number 0, 1
or 2, denoting the state (conformation trans/gauche). You can average the state of 100 molecules by
using average with “tors_state” as input file.
average tors_state frame-number > ave_tors_state
For example, if you ran 100000 steps, and recorded a frame every 50 steps, then the parameter framenumber
is 2000. You should obtain a file named as “ave_tors_state”. Use the program ccf to calculate
the autocorrelation function c (t)
defined below. However, “ave_tors_state” cannot directly be used as
input file for ccf, since ccf needs 3 columns, with the last two having the same value. Make an input
file for ccf (it expects 3columns) with “awk”.
awk ‘{print ($1, $2, $2)}’ ave_tors_state > ccf_input
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