Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: The canonical equilibrium of constrained molecular models   In order to increase the efficiency of the computer simulation of biological
molecules, it is very common to impose holonomic constraints on the fastest
degrees of freedom; normally bond lengths, but also possibly bond angles.
However, as any other element that affects the physical model, the imposition
of constraints must be assessed from the point of view of accuracy: both the
dynamics and the equilibrium statistical mechanics are model-dependent, and
they will be changed if constraints are used. In this review, we investigate
the accuracy of constrained models at the level of the equilibrium statistical
mechanics distributions produced by the different dynamics. We carefully derive
the canonical equilibrium distributions of both the constrained and
unconstrained dynamics, comparing the two of them by means of a "stiff"
approximation to the latter. We do so both in the case of flexible and hard
constraints, i.e., when the value of the constrained coordinates depends on the
conformation and when it is a constant number. We obtain the different
correcting terms associated with the kinetic energy mass-metric tensor
determinants, but also with the details of the potential energy in the vicinity
of the constrained subspace (encoded in its first and second derivatives). This
allows us to directly compare, at the conformational level, how the imposition
of constraints changes the thermal equilibrium of molecular systems with
respect to the unconstrained case. We also provide an extensive review of the
relevant literature, and we show that all models previously reported can be
considered special cases of the most general treatments presented in this work.
Finally, we numerically analyze a simple methanol molecule in order to
illustrate the theoretical concepts in a practical case.

23
The categories of this paper are: solv-int
14
The categories of this paper are: math-ph
33
The categories of this paper are: plasm-ph
27
The categories of this paper are: comp-gas
12
The categories of this paper are: nucl-th
20
The categories of this paper are: acc-phys
34
The categories of this paper are: chem-ph
22
The categories of this paper are: chao-dyn
1
The categories of this paper are: cs
13
The categories of this paper are: quant-ph
30
The categories of this paper are: q-alg
18
The categories of this paper are: econ
35
The categories of this paper are: mtrl-th
25
The categories of this paper are: patt-sol
0
The categories of this paper are: hep-ph
32
The categories of this paper are: atom-ph