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C. Tang (唐晨宇) and Y. Wang (王延颋)
5.4 Molecular Modeling
Before the implementation of a simulation, whether it is a Monte Carlo Simulation
or a Molecular Dynamics Simulation, it is necessary to define how the simulation
may be conducted. For all-atom simulations, the purpose of this is to treat a whole
atom as a single particle, which reduces the computational complexity and simplify
data analysis, leads to simulations with much larger temporal and spatial scales than
first-principles calculations, and allows investigations on system behaviors under a
finite temperature to be implemented. This requires the introduction of a force field
describing the interactions among atoms, and the method to provide an empirical
force field for a certain simulated system is called the molecular modeling method.
Normally, the molecular modeling method presets a functional form for the potential of two-body or many-body interactions with undetermined parameters, based on
the characteristics of the interactions between atoms. The parameters can fitted either
based on first-principles calculation data or experimental results. It should be noted
that in an all-atom simulation, it is impossible to accurately depict all properties in
a certain system when many degrees of freedom at the quantum level are reduced.
Thus, it is of much importance for researchers to find out the set of parameters to
determine, which coincides with the set of physical properties that researchers are
mostly interested in during the simulation, and the accuracy for other properties can
be loosened. The molecular model should be selected accordingly.
5.4.1 Reduced Unit
During the construction of certain molecular models and associated molecular simulations, it is useful to use the reduced unit instead of the SI-unit in the code to allow
most variables taking numeric values not far from 1, and thus to minimize numeric
truncation errors. The values can be recovered back to the SI-unit by multiplying a
constant. The common conversion of the reduced unit is stated as follows.
The units of up to four basic physical variables are required to deduce all the units.
If there are four units are given: length L, mass M , time t, and electric charge Q, we
can calculate the units of all other physical variables as
Energy:
E = M ∗ L
2
/t
2
(5.3.30)
Temperature:
T = E/k B
(5.3.31)
C. Tang (唐晨宇) and Y. Wang (王延颋)
5.4 Molecular Modeling
Before the implementation of a simulation, whether it is a Monte Carlo Simulation
or a Molecular Dynamics Simulation, it is necessary to define how the simulation
may be conducted. For all-atom simulations, the purpose of this is to treat a whole
atom as a single particle, which reduces the computational complexity and simplify
data analysis, leads to simulations with much larger temporal and spatial scales than
first-principles calculations, and allows investigations on system behaviors under a
finite temperature to be implemented. This requires the introduction of a force field
describing the interactions among atoms, and the method to provide an empirical
force field for a certain simulated system is called the molecular modeling method.
Normally, the molecular modeling method presets a functional form for the potential of two-body or many-body interactions with undetermined parameters, based on
the characteristics of the interactions between atoms. The parameters can fitted either
based on first-principles calculation data or experimental results. It should be noted
that in an all-atom simulation, it is impossible to accurately depict all properties in
a certain system when many degrees of freedom at the quantum level are reduced.
Thus, it is of much importance for researchers to find out the set of parameters to
determine, which coincides with the set of physical properties that researchers are
mostly interested in during the simulation, and the accuracy for other properties can
be loosened. The molecular model should be selected accordingly.
5.4.1 Reduced Unit
During the construction of certain molecular models and associated molecular simulations, it is useful to use the reduced unit instead of the SI-unit in the code to allow
most variables taking numeric values not far from 1, and thus to minimize numeric
truncation errors. The values can be recovered back to the SI-unit by multiplying a
constant. The common conversion of the reduced unit is stated as follows.
The units of up to four basic physical variables are required to deduce all the units.
If there are four units are given: length L, mass M , time t, and electric charge Q, we
can calculate the units of all other physical variables as
Energy:
E = M ∗ L
2
/t
2
(5.3.30)
Temperature:
T = E/k B
(5.3.31)