...
  • 主题
高级搜索  >
历史搜索 清空历史
首页> 外文期刊>Journal of chemical theory and computation: JCTC >Anomalous Effects of Velocity Rescaling Algorithms: The Flying Ice Cube Effect Revisited
【24h】

Anomalous Effects of Velocity Rescaling Algorithms: The Flying Ice Cube Effect Revisited

机译：速度重新扫描算法的异常效应：重新开始的飞行冰块效果

获取原文
获取原文并翻译 | 示例
           
页面导航
  • 摘要
  • 著录项
  • 相似文献
  • 相关主题

摘要

The flying ice cube effect is a molecular dynamics simulation artifact in which the use of velocity rescaling thermostats sometimes causes violation of the equipartition theorem, affecting both structural and dynamic properties. The reason for this artifact and the conditions under which it occurs have not been fully understood. Since the flying ice cube effect was first demonstrated, a new velocity rescaling algorithm (the CSVR thermostat) has been developed and become popular without its effects on the equipartition theorem being truly known. Meanwhile, the use of simple velocity rescaling and Berendsen (weak coupling) thermostat algorithms has not abated but has actually continued to grow. Here, we have calculated the partitioning of the kinetic energy between translational, rotational, and vibrational modes in simulations of diatomic molecules to explicitly determine whether the equipartition theorem is violated under different thermostats and while rescaling velocities to different kinetic energy distributions. We have found that the underlying cause of the flying ice cube effect is a violation of balance leading to systematic redistributions of kinetic energy under simple velocity rescaling and the Berendsen thermostat. When velocities are instead rescaled to the canonical ensemble's kinetic energy distribution, as is done with the CSVR thermostat, the equipartition theorem is not violated, and we show that the CSVR thermostat satisfies detailed balance. The critical necessity for molecular dynamics practitioners to abandon the use of popular yet incorrect velocity rescaling algorithms is underscored with an example demonstrating that the main result of a highly cited study is entirely due to artifacts resulting from the study's use of the Berendsen thermostat.
机译：飞行冰块效果是分子动力学模拟伪影，其中速度重新静音恒温器的使用有时会导致均方根定理侵犯结构和动态性质。本伪影的原因以及其发生的条件尚未得到完全理解。由于首先证明了飞冰立方体效应，因此已经开发了一种新的速度重新扫描算法（CSVR恒温器），而没有其对真正已知的ecipartition定理的影响而变得流行。同时，使用简单的速度重新扫描和Berendsen（弱耦合）恒温算法并未减少，但实际上继续增长。这里，我们已经计算了硅藻分子模拟中的平移，旋转和振动模式之间的动能的分配，以明确地确定ecipartition定理是否侵犯在不同的恒温器下，而在不同的动能分布中重新扫描速度。我们发现飞行冰块效应的潜在原因是违反了余额的平衡，导致简单的速度重新扫描和Berendsen恒温器下的动能的系统重新分配。当速度被重新分配到规范集合的动能分布时，与CSVR恒温器一样，ecipartition定理没有违反，我们表明CSVR恒温器满足详细的平衡。分子动力学医生放弃使用流行又不正确的速度重构算法的关键必要性是强调了展示高度引用的研究的主要结果完全是由于该研究使用Berendsen恒温器所产生的伪像。

著录项

相似文献

  • 外文文献
  • 中文文献
  • 专利
获取原文

客服邮箱：kefu@zhangqiaokeyan.com

京公网安备：11010802029741号 ICP备案号：京ICP备15016152号-6 六维联合信息科技 (北京) 有限公司©版权所有

  • 客服微信

  • 服务号