Vaidehi N, Jain A. Internal coordinate molecular dynamics: a foundation for multiscale dynamics.
J Phys Chem B 2015;
119:1233-42. [PMID:
25517406 PMCID:
PMC4315417 DOI:
10.1021/jp509136y]
[Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Internal coordinates such as bond
lengths, bond angles, and torsion
angles (BAT) are natural coordinates for describing a bonded molecular
system. However, the molecular dynamics (MD) simulation methods that
are widely used for proteins, DNA, and polymers are based on Cartesian
coordinates owing to the mathematical simplicity of the equations
of motion. However, constraints are often needed with Cartesian MD
simulations to enhance the conformational sampling. This makes the
equations of motion in the Cartesian coordinates differential-algebraic,
which adversely impacts the complexity and the robustness of the simulations.
On the other hand, constraints can be easily placed in BAT coordinates
by removing the degrees of freedom that need to be constrained. Thus,
the internal coordinate MD (ICMD) offers an attractive alternative
to Cartesian coordinate MD for developing multiscale MD method. The
torsional MD method is a special adaptation of the ICMD method, where
all the bond lengths and bond angles are kept rigid. The advantages
of ICMD simulation methods are the longer time step size afforded
by freezing high frequency degrees of freedom and performing a conformational
search in the more important low frequency torsional degrees of freedom.
However, the advancements in the ICMD simulations have been slow and
stifled by long-standing mathematical bottlenecks. In this review,
we summarize the recent mathematical advancements we have made based
on spatial operator algebra, in developing a robust long time scale
ICMD simulation toolkit useful for various applications. We also present
the applications of ICMD simulations to study conformational changes
in proteins and protein structure refinement. We review the advantages
of the ICMD simulations over the Cartesian simulations when used with
enhanced sampling methods and project the future use of ICMD simulations
in protein dynamics.
Collapse