Molecular Models

4.2 ls1 mardyn

The force field input for the simulation program ls1 mardyn consists of a single file with the extension .xml. Each .xml file contains the full specification of the force field. The file can be used directly without any further modifications by the simulation program. Unlike the pm file for ms2, a xml file can contain multiple models.

The data-layout of xml files is very similar to that of the pm files used for ms2. While the .pm file is structured by sections and keywords, the file has an xml format that makes sections obsolete. This is achieved by assigning the additional parameter type and ID to the individual interaction sites. To each individual model the additional parameters name and ID will be assigned to define multiple models simultaneously in one xml file. The following shows the full example for a ls1 input file for the molecular model of molecular model of hydrogen cyanide published by Eckl et al. [Eckl, 2008 C] :

<?xml version="1.0" encoding="UTF-8"?> <components version="06092018"> <moleculetype id="1" name="CHN"> <site type="LJ126" id="1"> <coords> <x>0.0</x> <y>0.0</y> <z>0.638</z> </coords> <sigma>3.233</sigma> <epsilon>39.69</epsilon> <mass>14.007</mass> </site> <site type="LJ126" id="2"> <coords> <x>0.0</x> <y>0.0</y> <z>-0.9671</z> </coords> <sigma>3.445</sigma> <epsilon>102.44</epsilon> <mass>13.018</mass> </site> <site type="Dipole" id="3"> <coords> <x>0.0</x> <y>0.0</y> <z>0.0589</z> </coords> <theta>180.0</theta> <phi>0.0</phi> <dipole>-3.4084</dipole> <mass>0.0</mass> </site> <site type="Quadrupole" id="4"> <coords> <x>0.0</x> <y>0.0</y> <z>0.0589</z> </coords> <quadrupolemoment> <theta>0.0</theta> <phi>0.0</phi> <abs>2.18</abs> </quadrupolemoment> <mass>0.0</mass> </site> <momentsofinertia rotaxes="xyz"> <Ixx>0</Ixx> <Iyy>0</Iyy> <Izz>0</Izz> </momentsofinertia> </moleculetype> </components>