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Music Tutorial - The atom atom file
The atom atom interactions are specified in this file. For each atom - atom pair the Lennard Jones interaction has to be specified in the following way.
[Atom1] [Atom2] LJ SIG@[no.] EPS@[no.] HICUT@[no.] LOCUT@[no.]e.g.
#Atom-Atom interaction file for methane in IRMOF1 using the UFF force field. Methane Oxygen LJ SIG@3.424 EPS@66.848 HICUT@12.8 Methane Carbon LJ SIG@3.580 EPS@88.431 HICUT@12.8 Methane Zinc LJ SIG@3.096 EPS@96.099 HICUT@12.8 Methane Hydrogen LJ SIG@3.151 EPS@57.245 HICUT@12.8 Methane Methane LJ SIG@3.730 EPS@148.000 HICUT@12.8 Oxygen Oxygen OFF Carbon Carbon OFF Hydrogen Hydrogen OFF Oxygen Carbon OFF Oxygen Hydrogen OFF Carbon Hydrogen OFF Zinc Zinc OFF
For the framework atom a standard force field is used that allows an atomistic description of all the framework atoms. The Lennard Jones parameters for the UFF force field can be found in:
Rappe et al. "UFF, a Full Periodic Table Force Field for Molecular Mechanics and Molecular Dynamics Simulations", Journal American Chemistry Society 1992, 114, 10024-10035
In this paper, a table with xi and Di is given which are converted as follows:
SIG = xi/2^(1/6)
EPS = Di/0.0019872
The mixed Lennard Jones parameters of the two interacting atoms (i and j) are calculated using Lorentz-Berthelot mixing rules:
SIGij = (SIGi + SIGj)/2
EPSij = sqrt(EPSi x EPSj)
HICUT is the cut-off radius. Any interactions between atoms that are further apart than HICUT will be neglected.
A value for LOCUT can be specified after the HICUT if you want but can be left blank and MUSIC will use a default value.
An example of anATOM-ATOM FILE