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1. Quick guide

For the sake of this quick guide, we provide here the necessary distribution files. These files would otherwise be obtained by running MD simulations.

Plase save these distribution files somewhere on your computer (right-click and select "Save link as ..."):

Step 1: Upload target distribution

In this step we will upload the target atomistic distribution.

The file is uploaded and its data is displayed in the left chart. The initial guess potential is automatically generated and displayed in the right chart. The corresponding potential file pot-rdf_cgcg_tgt_0 is displayed in the Potential input box. We could use this file to run a simulation, however, we will first smoothen the target distribution file and regenerate the potential. This is done in the next step.

Smoothing data

Now we will smoothen the target atomistic distribution data and regenerate the initial guess potential. Smoothing is not always necessary, but we will do it for the sake of this tutorial.

You may zoom on the chart by scrolling your mouse wheel. To move around (pan) click and drag the chart.

Smoothing and interpolation of data points is possible in two separate ranges. The range input boxes have a minimum and maximum value (from - to). In this example, we will smooth in the range 1.0 - 3.5.

We leave all other options as they are. If you wish, you are of course free to play with different parameters. The effects are immediately shown on the chart.

We will use the smoothed file to regenerate the initial potential guess.

In the next step, we will download this file and use it to run a short coarse-grained simulation.

Step 2: Download potential, run simulation

In this step we will download the initial potential guess file and run a short coarse-grained simulation.

This is a tabulated potential file defining interactions between coarse-grained water molecules. You may run a simulation with this file now, but to save you time, we have already done that.

In the next step we will upload the obtained radial distribution funtions.

Step 3: Upload obtained distribution

In this step we will upload the radial distribution funtion obtained from our coarse-grained simulation with the initial guess potential.

The distribution appears on the left chart. Since it does not match the target distribution, we have to refine the potential.

Proceed to the next step where we will generate a new iteration of the potential.

Step 4: Generate new potential

In this step we will generate a new potential by refining the current potential.

In the next step we repeat the process until the obtained distribution matches the target distribution.

Repeat steps 2, 3, and 4

We now repeat the process of running coarse-grained simulations, uploading the obtained distribution and generating new potentials. Since we have already calculated the distributions, you do not have to run the simulations.

We run a coarse-grained simulation with the new potential and upload the obtained distribution file. Repeat the above steps for the remaining files you saved: rdf_cgcg_2 and rdf_cgcg_3.

This is all for this quickguide. Happy coarse-graining! Press next, to return to first page.

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