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 ..."):
In this step we will upload the target atomistic distribution.
Click on the plus button (+) under the Target distribution input box.
Browse to the file rdf_cgcg_tgt you have downloaded before, and select it.
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.
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.
Select the rdf_cgcg_tgt file in the Target distribution input box, and click on the Smoothen button below. A window opens showing both the original and the smoothed data.
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.
Click on the minumum value of range1. The range is drawn on the chart. Set the value to 1.0.
Click on the maximum value of range1. Set the value to 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.
Click on the Accept button. The smoothing window closes, and a new file rdf_cgcg_tgt_smt appears in the target distribution input box.
We will use the smoothed file to regenerate the initial potential guess.
Select the file rdf_cgcg_tgt_smt and click on the Generate potential button. This generates a new initial guess potential file.
In the next step, we will download this file and use it to run a short coarse-grained simulation.
In this step we will download the initial potential guess file and run a short coarse-grained simulation.
Select the pot-rdf_cgcg_tgt_smt_0 file in the Potential input box, and click on the Download button below. Save the file somewhere on your computer.
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.
In this step we will upload the radial distribution funtion obtained from our coarse-grained simulation with the initial guess potential.
Click the plus button (+) under the Obtained distribution input box.
Select the file rdf_cgcg_0, which you have saved at the beginning of this guide (this file would otherwise be obtained from your simulation).
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.
In this step we will generate a new potential by refining the current potential.
Select the target distribution, obtained distribution and potential in their corresponding input boxes by clicking on them (in our case these are rdf_cgcg_tgt_smt, rdf_cgcg_0 and pot-rdf_cgcg_tgt_smt_0).
Note: if you click a selected file, it becomes deselected.
Click the Generate potential button. A new potential file is generated and ready to be downloaded.
In the next step we repeat the process until the obtained distribution matches the target distribution.
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.
Click the plus button (+) under the Obtained distribution input box.
Select the file rdf_cgcg_1, which you have saved at the beginning of this guide.
Since it does not match the target distribution, we have to refine the potential.
Select the corresponding target distribution, obtained distribution, potential and press the Generate potential button. A new potential file is generated and ready to be downloaded.
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.