Tina Düren

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Department of Chemical Engineering, University of Bath

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Music Tutorial - The molecule file

The molecule file describes the shape of the molecule and how the individual Lennard Jones spheres that it cosists of are connected. You should store all your atom files in one central directory, which you specify in your environment file.

Methane consists of a single Lennard Jones sphere (united atom approach), its molecule file is rather simple:

### Methane Molecule File

Molecule_Name:  Methane
          
Coord_Info: Listed Cartesian Rigid 
    1     # number of atoms in molecule 
    1    0.000000    0.000000    0.000000      Methane   0.0  0   0   #x,y,z,name,set,type 

The position of all LJ spheres are listed and given in cartesian coordinates, 
the molecule is treated as rigid 
  

A more complex example is butane which is represented by two CH3 and two CH2 spheres:

##### Basic Molecule Information

Molecule Name: Butane 

Coord_Info: Listed Cartesian Branched 

        4     # number of atoms in molecule
        1    0.000000     0.000000    0.000000            Methyl        0.0 0  0    #x,y,z,name,set,type 
        2    1.268427    -0.855565    0.000000            Methylene     0.0 0  0    #x,y,z,name,set,type
        3    2.536855     0.000000    0.000000            Methylene     0.0 0  0    #x,y,z,name,set,type
        4    3.805282    -0.855565    0.000000            Methyl        0.0 0  0    #x,y,z,name,set,type

The first coloumn is the atom number followed by its position in x,y,z cartesian coordinates. Next is the atom that is in this position. In the case of butane two solid sphere 'atoms' are used, CH3 Methyl and CH2 Methylene

Connect_Info: Generate
    2    # number of connection types listed
    Methyl          Methylene  1.530000
    Methylene     Methylene    1.530000

In this case the bonds are generated automatically. You could also specify the connections explicitly by using the "Listed" instead of the "Generate" keyword.

##### Intramolecular forces

Bond_Bending: Listed Harmonica Fast
    2  # number of bending centers 
    1    2    3  124.200000  114.000000 # atoms, k(kcal/mol), thetaeq (deg)
    2    3    4  124.200000  114.000000   

Bond_Torsion: Listed Cosexpansion Fast
    1     # number of torsion angles
   1  2  3  4  2.00642   4.01084    0.27092   -6.28819   0.0000     0.000000  

If butane is treated as a flexible molecule, bond bending and torsion will be taken into account. The force field parameters are specified in the molecule file.


For the framework, you have to get / create a similar file that contains the x,y,z (Cartesian) coordinates of ALL (= after the symmetry operations have been applied) the framework atoms including the hydrogens. Xyz files can be obtained from cif files, the file format that most published structures are given.

An example of a MOLECULE FILE