Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Replica-Permutation Method with the Suwa-Todo Algorithm beyond the
  Replica-Exchange Method   We propose a new method for molecular dynamics and Monte Carlo simulations,
which is referred to as the replica-permutation method (RPM), to realize more
efficient sampling than the replica-exchange method (REM).In RPM not only
exchanges between two replicas but also permutations among more than two
replicas are performed. Furthermore, instead of the Metropolis algorithm, the
Suwa-Todo algorithm is employed for replica-permutation trials to minimize its
rejection ratio. We applied RPM to particles in a double-well potential energy,
Met-enkephalin in vacuum, and a C-peptide analog of ribonuclease A in explicit
water. For a comparison purposes, replica-exchange molecular dynamics
simulations were also performed. As a result, RPM sampled not only the
temperature space but also the conformational space more efficiently than REM
for all systems. From our simulations of C-peptide, we obtained the
\alpha-helix structure with salt-bridges between Gly2 and Arg10 which is known
in experiments. Calculating its free-energy landscape, the folding pathway was
revealed from an extended structure to the \alpha-helix structure with the
salt-bridges. We found that the folding pathway consists of the two steps: The
first step is the "salt-bridge formation step", and the second step is the
"\alpha-helix formation step".

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The categories of this paper are: bayes-an
19
The categories of this paper are: eess
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The categories of this paper are: atom-ph
9
The categories of this paper are: nlin
0
The categories of this paper are: hep-ph
18
The categories of this paper are: econ
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The categories of this paper are: acc-phys
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The categories of this paper are: chao-dyn
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The categories of this paper are: dg-ga
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The categories of this paper are: hep-th
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The categories of this paper are: stat
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The categories of this paper are: funct-an
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The categories of this paper are: nucl-ex
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The categories of this paper are: math-ph
5
The categories of this paper are: gr-qc
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The categories of this paper are: q-alg