Molecular dynamics sampling scheme realizing multiple distributions

被引:5
作者
Fukuda, I
Nakamura, H
机构
[1] Natl Inst Adv Ind Sci & Technol, Koto Ku, Tokyo 1350064, Japan
[2] Osaka Univ, Inst Prot Res, Suita, Osaka 5650871, Japan
来源
PHYSICAL REVIEW E | 2005年 / 71卷 / 04期
关键词
D O I
10.1103/PhysRevE.71.046708
中图分类号
O35 [流体力学]; O53 [等离子体物理学];
学科分类号
070204 ; 080103 ; 080704 ;
摘要
We present a molecular-dynamics sampling scheme in which any summation of multiple arbitrarily given distributions can be realized deterministically by a certain theoretical guide. Our scheme thus provides a static view of the composition of the distributions, rather than a dynamic view in which some parameter is switched at a certain time in the simulation process. The proposed method induces the orbit to jump automatically among different phase space regions, without the use of any artificial timing parameter. In addition, the proposed method does not require an assumption that the density of states is smooth. We applied it to multiple Tsallis distributions and established a suitable series of parameter values for which the sum of the distributions allows broad sampling. Numerical simulations applied to fundamental models with multi-Tsallis distributions showed efficient sampling, characterized by an energy trajectory that was totally different from that associated with each single distribution.
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页数:13
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共 57 条
[1]   Partition function zeros and finite size scaling of helix-coil transitions in a polypeptide [J].
Alves, NA ;
Hansmann, UHE .
PHYSICAL REVIEW LETTERS, 2000, 84 (08) :1836-1839
[2]   Extended phase-space dynamics for the generalized nonextensive thermostatistics [J].
Andrade, JS ;
Almeida, MP ;
Moreira, AA ;
Farias, GA .
PHYSICAL REVIEW E, 2002, 65 (03)
[3]   On monte carlo and molecular dynamics methods inspired by Tsallis statistics: Methodology, optimization, and application to atomic clusters [J].
Andricioaei, I ;
Straub, JE .
JOURNAL OF CHEMICAL PHYSICS, 1997, 107 (21) :9117-9124
[4]   Self-guided enhanced sampling methods for thermodynamic averages [J].
Andricioaei, I ;
Dinner, AR ;
Karplus, M .
JOURNAL OF CHEMICAL PHYSICS, 2003, 118 (03) :1074-1084
[5]  
[Anonymous], 1997, Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications
[6]   Generalization of the Nose-Hoover approach [J].
Branka, AC ;
Kowalik, M ;
Wojciechowski, KW .
JOURNAL OF CHEMICAL PHYSICS, 2003, 119 (04) :1929-1936
[7]   A 2ND GENERATION FORCE-FIELD FOR THE SIMULATION OF PROTEINS, NUCLEIC-ACIDS, AND ORGANIC-MOLECULES [J].
CORNELL, WD ;
CIEPLAK, P ;
BAYLY, CI ;
GOULD, IR ;
MERZ, KM ;
FERGUSON, DM ;
SPELLMEYER, DC ;
FOX, T ;
CALDWELL, JW ;
KOLLMAN, PA .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1995, 117 (19) :5179-5197
[8]   Conformational dynamics in a dipeptide after single-mode vibrational excitation [J].
Dian, BC ;
Longarte, A ;
Zwier, TS .
SCIENCE, 2002, 296 (5577) :2369-2373
[9]   Diffusion in metallic glasses and supercooled melts [J].
Faupel, F ;
Frank, W ;
Macht, MP ;
Mehrer, H ;
Naundorf, V ;
Rätzke, K ;
Schober, HR ;
Sharma, SK ;
Teichler, H .
REVIEWS OF MODERN PHYSICS, 2003, 75 (01) :237-280
[10]   NEW MONTE-CARLO TECHNIQUE FOR STUDYING PHASE-TRANSITIONS [J].
FERRENBERG, AM ;
SWENDSEN, RH .
PHYSICAL REVIEW LETTERS, 1988, 61 (23) :2635-2638