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Journal of Chemical Physics / Volume 123 / Issue 17 / ARTICLES / Polymers, Biopolymers, and Complex Systems

J. Chem. Phys. 123, 174905 (2005); http://dx.doi.org/10.1063/1.2102896 (7 pages)

Efficient Monte Carlo trial moves for polypeptide simulations

Marcos R. Betancourt

Department of Physics, Indiana University Purdue University Indianapolis, Indianapolis, Indiana 46202

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(Received 12 July 2005; accepted 8 September 2005; published online 31 October 2005)

A new move set for the Monte Carlo simulations of polypeptide chains is introduced. It consists of a rigid rotation along the (Cα) ends of an arbitrary long segment of the backbone in such a way that the atoms outside this segment remain fixed. This fixed end move, or FEM, alters only the backbone dihedral angles ϕ and ψ and the Cα bond angles of the segment ends. Rotations are restricted to those who keep the α bond angles within their maximum natural range of approximately ±10°. The equations for the angular intervals (τ) of the allowed rigid rotations and the equations required for satisfying the detailed balance condition are presented in detail. One appealing property of the FEM is that the required number of calculations is minimal, as it is evident from the simplicity of the equations. In addition, the moving backbone atoms undergo considerable but limited displacements of up to 3 Å. These properties, combined with the small number of backbone angles changed, lead to high acceptance rates for the new conformations and make the algorithm very efficient for sampling the conformational space. The FEMs, combined with pivot moves, are used in a test to fold a group of coarse-grained proteins with lengths of up to 200 residues.

© 2005 American Institute of Physics

Article Outline

  1. INTRODUCTION
  2. FIXED ENDS MOVE
  3. COARSE-GRAINED PROTEIN MODEL
  4. THE REMAINING ELEMENTS OF THE MONTE CARLO ALGORITHM
  5. FOLDING TESTS
  6. SUMMARY

ERRATA AND EDITORIALLY RELATED

    Related Articles

  1. Comment on “Efficient Monte Carlo trial moves for polypeptide simulations” [J. Chem. Phys. 123, 174905 (2005)]
    Alexei A. Podtelezhnikov et al.
    J. Chem. Phys. 129, 027103 (2008)JCPSA6000129000002027103000001

    2. Erratum

  2. Erratum: “Efficient Monte Carlo trial moves for polypeptide simulations” [J. Chem. Phys. 123, 174905 (2005)]
    Marcos R. Betancourt
    J. Chem. Phys. 129, 019903 (2008)JCPSA6000129000001019903000001

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KEYWORDS and PACS

Keywords

proteins, molecular biophysics, bond angles, Monte Carlo methods, rotational states

PACS

ARTICLE DATA

Digital Object Identifier
http://dx.doi.org/10.1063/1.2102896

PUBLICATION DATA

ISSN

0021-9606 (print)  
1089-7690 (online)

Publisher

$abstract.society.value is a Member of CrossRef American Institute of Physics

For access to fully linked references, you need to log in.
    N. Metropolis, A. W. Rosenbluth, M. N. Rosenbluth, and A. H. Teller, J. Chem. Phys. 21, 1087 (1953)JCPSA6000021000006001087000001.

    J. Schofield and M. A. Ratner, J. Chem. Phys. 109, 9177 (1998)JCPSA6000109000020009177000001.

    M. R. Betancourt, J. Chem. Phys. 109, 1545 (1998)JCPSA6000109000004001545000001.

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    G. Favrin, A. Irbäck, and F. Sjunnesson, J. Chem. Phys. 114, 8154 (2001)JCPSA6000114000018008154000001.

    J. P. Ulmschneider and W. L. Jorgensen, J. Chem. Phys. 118, 4261 (2003)JCPSA6000118000009004261000001.


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