Running metropolis_pl

Now you understand the algorithm, please run the metropolis_pl Monte Carlo program again using the command;

$ perl metropolis_pl

Watch what is printed out (the move number, then the total energy, then the number of accepted moves, then the number of rejected moves), e.g.

10: 263471.098167728  5   5
20: 114030.78800927  11   9
30: 5999.19636795258  17   13
40: 4719.87647170638  26   14
50: 4686.88406567588  31   19
60: 539.640252029864  37   23
70: 388.498103662198  43   27
80: 279.303981060543  51   29
90: 257.443473831169  60   30
100: 255.040363808318  68   32

Keep running the program until is has finished. It will produce a lot of PDB output coordinate files, called output??????.pdb. View these files in VMD. You can make a movie of these files in Linux by typing;

$ vmd output*.pdb

If you are using Windows, then you have to create a VMD animation script. You can do this by downloading the script animatepdb_pl. Then type;

$ perl animatepdb_pl output*.pdb > movie.vmd

Open VMD, then use the Tcl shell to change into the directory that contains movie.vmd. In the Tcl shell then type;

play movie.vmd

The movie is of a periodic box of krypton. To see the periodic cells, open the "Graphical Representations" window in VMD and select the "Periodic" tab. Under "Select periodic images to draw" click the "+X", "-X", "+Y", "-Y", "+Z" and "-Z" boxes. This will display those periodic images. Click on the "Play" icon in the "VMD Main" window to play the movie.