The improvement of the algorithm for order parameter calculation (S-2) from molecular dynamics simulation using the correlation motion function

Dubyna VM; Kovalskyy DB; Ivanova OS; Kornelyuk AI

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The improvement of the algorithm for order parameter calculation (S-2) from molecular dynamics simulation using the correlation motion function

机译：使用相关运动函数的分子动力学模拟对顺序参数计算（S-2）算法的改进

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The generalized order parameter, S-2, calculated from MD simulation trajectory using time-dependent internal Correlation Motion Function (CMF) agrees well with NMR derived S-2 processed with the extended model-free analysis approach. However, the former lies considerably lower comparing to simple model-free derived data from NMR experiments. In the present study we analyze possible reasons of such disagreement. In the general case we propose to use preexponential factors from expression for internal CMF rather than ordinary S values. Particularly, in case of the simple model-free S-2 experimental values we suggest comparing them with S-eff(2)=1+S-2-S-f(2) computed from MD simulation data. We show that the S-eff(2) values are in a good agreement with NMR derived S-2 values obtained using the simple model-free analysis. (c) 2006 Elsevier B.V. All rights reserved.

机译：使用与时间相关的内部相关运动函数（CMF）从MD模拟轨迹计算出的广义阶数参数S-2与使用扩展的无模型分析方法处理的NMR得出的S-2非常吻合。但是，与来自NMR实验的简单无模型导出数据相比，前者要低得多。在本研究中，我们分析了这种分歧的可能原因。在一般情况下，我们建议对内部CMF使用表达式中的指数前因子，而不是普通S值。特别是，在简单的无模型S-2实验值的情况下，我们建议将其与从MD仿真数据计算出的S-eff（2）= 1 + S-2-S-f（2）进行比较。我们表明，S-eff（2）值与使用简单的无模型分析获得的NMR得出的S-2值非常一致。（c）2006 Elsevier B.V.保留所有权利。

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《Biophysical Chemistry: An International Journal Devoted to the Physical Chemistry of Biological Phenomena》 |2006年第1期|共4页
作者
Dubyna VM; Kovalskyy DB; Ivanova OS; Kornelyuk AI;
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正文语种 eng
中图分类生物化学;
关键词
internal correlated motion function; S-2 order parameter; MD simulation; the NMR relaxation data; extended model-free analysis; simple model-free analysis; INTERLEUKIN-1-BETA; SPECTROSCOPY; FLUCTUATIONS; RELAXATION; LYSOZYME;

机译：内部相关运动函数;S-2阶参数;MD模拟;核磁共振弛豫数据;扩展无模型分析;简单无模型分析;白介素-1-BET;光谱学;波动;松弛;溶菌酶;

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机译：使用相关运动函数的分子动力学模拟对顺序参数计算（S-2）算法的改进
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The improvement of the algorithm for order parameter calculation (S-2) from molecular dynamics simulation using the correlation motion function

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