Report
Acceleration of Mean Square Distance Calculations with Floating Close Structure in Metadynamics Simulations
| العنوان: | Acceleration of Mean Square Distance Calculations with Floating Close Structure in Metadynamics Simulations |
|---|---|
| المؤلفون: | Pazúriková, Jana, Oľha, Jaroslav, Křenek, Aleš, Spiwok, Vojtěch |
| سنة النشر: | 2018 |
| المجموعة: | Computer Science |
| مصطلحات موضوعية: | Computer Science - Computational Engineering, Finance, and Science, Computer Science - Distributed, Parallel, and Cluster Computing, Computer Science - Numerical Analysis, 68W25 68U20 65Y20 70-08 70F10 |
| الوصف: | Molecular dynamics simulates the~movements of atoms. Due to its high cost, many methods have been developed to "push the~simulation forward". One of them, metadynamics, can hasten the~molecular dynamics with the~help of variables describing the~simulated process. However, the~evaluation of these variables can include numerous mean square distance calculations that introduce substantial computational demands, thus jeopardize the~benefit of the~approach. Recently, we proposed an~approximative method that significantly reduces the~number of these distance calculations. Here we evaluate the~performance and the~scalability on two molecular systems. We assess the~maximal theoretical speed-up based on the reduction of distance computations and Ahmdal's law and compare it to the~practical speed-up achieved with our implementation. Comment: 22 pages, 5 figures |
| نوع الوثيقة: | Working Paper |
| URL الوصول: | http://arxiv.org/abs/1801.02362 |
| رقم الانضمام: | edsarx.1801.02362 |
| قاعدة البيانات: | arXiv |
| الوصف غير متاح. |