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Оценка профилей потенциала средней силы методом Umbrella sampling для трансмембранного переноса водыстатья
Дата последнего поиска статьи во внешних источниках: 3 ноября 2021 г.
- Авторы: Антонов М.Ю., Науменкова Т.В., Попинако А.В., Николаев И.Н., Шайтан К.В.
- Журнал: Математические заметки СВФУ
- Том: 21
- Номер: 3
- Год издания: 2014
- Первая страница: 96
- Последняя страница: 106
- Аннотация: Abstract. Modeling the passive transmembrane transport of small molecules by molec- ular modeling methods faces a series of difficulties because in the available modeling time it is practically impossible to observe the process of spontaneous diffusion and measure its averaged macroscopic characteristics. Therefore, of interest are those approaches and methods that we can use to get in reasonable time the results enabling us to make comparative studies or comparisons with natural experimental data. We use the methods of controlled molecular dynamics and umbrella sampling to study the process of transmembrane transport of water molecules through a lipid bilayer. We use a bilayer of 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine (ДМФХ) (DMPC) in the force field OPLS-AA. We construct the middle force profiles from the calculated data with trajectories of length 6–10 ns. We compare the resulting profiles for vari- ous spatial positions of the test water molecule (permeating through the bilayer), for different steps of the choice of original configurations, and for various initial values of the velocity of atoms in the system. The total modeling time was more than 10 ms. We demonstrate a significant dependence of the results of calculations on initial data and the simulation protocol. In the framework of this approach we estimate the kinetic permeability parameters and the potential of an average force, as well as study the de- pendence of the calculated values on the initial data of the simulation. We estimate the accuracy of the calculation basing on the analysis of a series of simulations. Keywords: molecular modeling, umbrella sampling method, biomembranes
- Добавил в систему: Шайтан Константин Вольдемарович
Прикрепленные файлы
| № | Имя | Описание | Имя файла | Размер | Добавлен |
|---|---|---|---|---|---|
| 1. | Полный текст | english | Antonov.pdf | 343,0 КБ | 10 мая 2015 [ShaitanKV] |
| 2. | Полный текст | русский текст | scan-mz.pdf | 10,1 МБ | 11 мая 2015 [ShaitanKV] |