MUSIC Tutorial

Atom-Atom interaction 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.

   
#This is the Atom-Atom interaction file for a methane in IRMOF1 simulation 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 x_i and D_i 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

The 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 ATOM-ATOM FILE