Biology Reference
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solvated molecule. If the solvent can be treated in this manner, the
number of particles that must be simulated can be significantly
reduced. However, these models have their deficiencies and are known
to fail in predicting the structure and thermodynamics for certain types
of solvated molecules [13].
An alternative to implicit solvent models is the use of an explicit
molecular model for the solvent. Explicit solvent models treat the
solvent as a large number of discrete molecules interacting with the
solute. Several accurate force fields exist for the simulation of a hand-
ful of solvent types. The most studied solvent is water, and there are
several popular fixed charge force fields for this important solvent,
including SPC [14], TIP3P, TIP4P [15], SPC/E [16], TIP5P [17], and
TIP4P-Ew [18]. Several water force fields that include polarization
effects are under active development and testing. Although polarizable
models show a lot of promise, at this time they have not been fully
proven in terms of their accuracy in the context of large biomolecular
simulations on proteins.
After force field quality, the second major challenge for the field
of simulation relates to the time scale of the biophysical processes of
interest. One can see from figure 3.4 that bond vibrations have periods
measured in tens of femtoseconds (fs; 1 femtosecond
10 −15 seconds).
This fast motion determines the time scale for MD time step sizes.
Typically, time step sizes are in the range of 0.5 to 2.0 fs. Simulations
with time step sizes of 2.0 fs require the bond vibrations to be frozen,
=
Figure 3.4 A hierarchy of representative time scales for processes in biological
systems.
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