Special atoms
Format: string
Default: None
Description: nMOLDYN will create the MMTK universe with the atom names specified in the FIELD file.
By default, nMOLDYN will interpret these names directly as if they were a chemical symbol. If this fails,
nMOLDYN will remove the last character until it corresponds to a known chemical symbol. For example, an
atom defined in the FIELD file as CB, will first be interpreted as an atom of chemical symbol CB. As it does not
exist, nMOLDYN will interpret it as an atom of chemical symbol C, namely a carbon atom. Usig htis procedure,
it can happen that some atom names can be misunderstood or event not understood at all by MMTKAs an example, the figure 4.7 shows the example of a FIELD file
where one carbon atom specification (the one in red in the figure) will be misinterpreted as a cesium atom.
Figure 4.7:
Example of a DL_POLY/FIELD file for which the Special atoms field must be
filled because one carbon atom name, CS, will be interpreted as a cesium atom.
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The aim of the Special atoms field is precisely to avoid such problems. The format for the
Special atoms field is
atom name1:element1 sep atom name2:element2 ... where sep can be a white space, a comma or a semicolon.
In the example showed in figure 4.7, the string CS:C should be entered in the Special atoms field.
Interestingly, the Special atoms field can also be used to specify united atoms. The syntax is exactly the same but, in
that case, the element name must be replaced by the MMTK united atom code (e.g. CH3, CH2, CH, NH, NH2, NH3, OH, SH ...).