Molecular Dynamic Simulation of united atom liquid n-hexane

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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 6
THEORETICAL PHYSICAL CHEMISTRY TU DARMSTADT You can finally get the autocorrelation function of the torsion state: ccf ccf_output Use xmgrace ccf_output to view it. Autocorrelation function for torsion state: ( h( t) − h )( h( 0) . c( t) = ( h( t) − h where h(t) is the respective state (trans/gauche) at time t . 4. Follow the same procedure to calculate the other two c(t). (central torsion (tor2.dat) and the other end torsion (tor3.dat)). For all the repeated commands, you can make a shell script program to run in torsion2 and torsion 3. Plot the result for every torsion on separate graphs. Plot the three results in a single figure where you will restrict the time-scale to an interval where the decrease of the curves can clearly be seen. 5. Compute the distribution of the torsion angles. This can be done by applying the tool distribtors. That program reads the file resultfile produced previously. Copy from the directory /data/home/fleroy/students/exercises/prace4/ the program distribtors to the three directories you have created for each torsion. Run it by simply typing ./distribtors The program will ask you for the number of lines in resultfile. This can be obtained by a UNIX command: wc –l resultfile Or more directly by multiplying the number of frames written in the trajectory file by the number of molecules. You will collect a file named tors_angl_dist.dat which contains the probability distribution of finding an angle having a given value for the considered torsion. Plot the results in a single figure so as to compare them. 6. Calculate the center-of-mass diffusion coefficient First with cmtrj create the center of mass trajectory. Use msd to obtain the mean square displacement from the trajectory. And then compute the diffusion coefficient using diffcoeff. Both the programs msd and cmtrj need separate template files. We set msd.tpl as the template file for msd, and cm.tpl as that for cmtrj. First, create cm.tpl with the YASP tool mkcmtrjtemplate cm.tpl 2 ) − h ) 7
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Molecular Dynamic Simulation of united atom liquid n-hexane

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