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Please refer to Sampling Method section in order to familiarise with the simulation options available from the Applet.
Descriptions of MC Applet buttons:
Run/Stop: Button that starts or stops running simulation.
Step: Stop after running one MC cycle.
Restart: Restart simulation, using the original set of simulation parameters. Note: When the New button is pressed the current parameters set will become
the original set.
New: Button that runs a new simulation using the new parameter sets, as specified by the user.
Relax: Number of MC cycle that will be executed at the beginning of a simulation before the sampling is taken place. This ensures that the initial structure is properly 'relaxed'. This number should be larger the longer the chain and/or the lower the temperature.
Sample: Number of MC cycle during sampling stages. The longer the chain the larger this value should set. As a rough guide, you need about 10000 cycle for N=40 and 100000 cycles for N=100 for good statistics. (Much larger values may have to use to get research-grade results).
Display: This number determines number of MC cycles that will be executed before the image chain is updated. It also determines the sampling intervals, that is, a result is calculated and sampled once every Display number of MC cycles. By default, this is set to 5.
Scale image: Scale the size of image chain.
Image and Beads: These checkboxes control how an image is displayed. Note: by switching the Image to 'off' computational resources will be dedicated to run simulations and much shorter time will be taken to complete a simulation.
On the image screen, some values are also shown which are listed below:
Acceptance: This indicates the percentage of new chains (with portions of new-grown beads) that has been accepted. This is a rough indication how efficient the MC is performing.
Deviation: This is a statistical quantity that shows the variation of <s2> that has been sampled so far.
The value of <s2> (shown as <s^2>) is the average value, while the s2(shows as s^2) at the bottom image screen corresponds to the current chain shown on screen.
When the MCPoly applet is first run, a chain is randomly generated, based on the default parameters as shown on the right. The values can be edited as wishes and can be done only when a simulation is stopped. You can actually start a mini research project by running a chain length at different temperatures: (i) Run simulations and obtain <s2> for each temperature.(ii) Plot the results of <s2> versus temperature. You should
get a curve showing coil-globule transition. Repeat the simulations for different chain lengths to get different coil-globule transition curves. What do you find?
Useful tips:
You can repeat a simulation several times (say 5 times) for a given chain length and temperature, and get the average result. This will improve both the statistics and the accuracy.
Wish you a happy simulating!
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