Generating a molecular structure with the SetModel
Generating a file with the XYZ format
Generating a file with the TXYZ format
In this page, we explain which file formats we can use for describing the structural data of tips and samples in the SPM simulator.
Moreover, we explain how to prepare files with these file formats.
Reading this page, you can confirm which file format is suitable for each solver.
Reading this page, you can learn how to prepare an input data file which is organized in the specified file format.
SetModel is software developed by Advanced Algorithm & Systems Co., Ltd.
ChemSketch is provied as freeware and you can download it from this web page.
OpenBabel is provided as freeware and you can download from this web page.
| Solver | PDB file format | Image file formats (PNG, BMP, JPG) |
CUBE file format | XYZ file format | TXYZ file format |
|---|---|---|---|---|---|
| GeoAFM, FemAFM |
OK | OK | OK | OK | OK |
| CG, MD |
OK | ||||
| DFTB | OK | OK |
[How to prepare file formats]
The PDB file format
The PDB file format describes structural data of proteins.
Structural data of various proteins are provided as the PDB file format in the Protein Data Bank
http://www.rcsb.org/pdb/home/home.do.
Please download a PDB file of a protein that you want to simulate.
To perform simulations with GeoAFM and FemAFM,
you can use files of grayscale images for the structural data of tips and samples.
Files of grayscale images with PNG, BMP, and JPG file formats are available.
You can generate image files with PNG, BMP, and JPG file formats with image editors, for example, GIMP.
Details of how to prepare structural data of tips and samples with grayscale image files are explained
on page 24 in case examples of the SPM simulations.
The CUBE file format is a special structural data for the SPM simulator.
Analyzer can process experimental image data and save them as the CUBE file format.
How to use the Analyzer is explained in the tutorial of the SPM simulator.
There are two methods for preparing files in the XYZ and TXYZ formats as follows:
Details of the first method above are explained in the tutorial of the SPM simulator.
Details of the second method above are explained in the tutorial of the SPM simulator.
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(The method No. 1)
Generating a molecular structure with the SetModel |
|
Generating a file with the XYZ format
Generating a file with the TXYZ format
|
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(The method No. 2)
Generating a molecular structure with the ChemSketch |
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A file with the MOL format |
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Transforming the file format with the OpenBabel |
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Generating a file with the XYZ format
Generating a file with the TXYZ format
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If you cannot find a suitable simulation tool for your purpose, please contact us by e-mail.
When you send an e-mail to us, a string of characters is put into a subject of the e-mail automatically.
This string tells us at which stage of the simulation you have a trouble.
