Molecular Dynamic Simulation of united atom liquid n-hexane

THEORETICAL PHYSICAL CHEMISTRY TU DARMSTADT
Then extract the center of mass trajectory file by:
cmtrj md.trj cm.trj < cm.tpl
To create msd.tpl, type:
echo 1 1> msd.tpl
then use msd and diffcoeff to calculate the diffusion coefficient of n-hexane. (Remember, calculate
msd.dat from the center of mass trajectory)
7. Modifying the torsion potential.
An important advantage of the simulation approach is that it allows tuning force-field parameters in
order to understand related mechanisms.
Here, you are proposed to modify the coefficients of the torsion potential and probe the effect of such a
change on the torsion dynamics, the torsion angle distribution as well as on the mass density and the
diffusion coefficient.
Create a new directory where you will run the same simulation as previously but using a different
torsion potential. Use the same initial coordinates file, the same MD parameters files and the same
topology file where you will have replaced the torsion potential coefficients
K1 = 9.8 kJ/mol, K2 = 6.6 kJ/mol, and K3 = 10.6 kJ/mol
by
K´1 = 5.9037kJ/mol, K´2 = -1.13386 kJ/mol, and K´3 = 13.15868 kJ/mol .
Run the different steps (equilibration and production). Analyze the production trajectory the same way.
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