کد مقاله | کد نشریه | سال انتشار | مقاله انگلیسی | نسخه تمام متن |
---|---|---|---|---|
6919547 | 863698 | 2016 | 7 صفحه PDF | دانلود رایگان |
عنوان انگلیسی مقاله ISI
Martini straight: Boosting performance using a shorter cutoff and GPUs
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موضوعات مرتبط
مهندسی و علوم پایه
شیمی
شیمی تئوریک و عملی
پیش نمایش صفحه اول مقاله
چکیده انگلیسی
In molecular dynamics simulations, sufficient sampling is of key importance and a continuous challenge in the field. The coarse grain Martini force field has been widely used to enhance sampling. In its original implementation, this force field applied a shifted Lennard-Jones potential for the non-bonded van der Waals interactions, to avoid problems related to a relatively short cutoff. Here we investigate the use of a straight cutoff Lennard-Jones potential with potential modifiers. Together with a Verlet neighbor search algorithm, the modified potential allows the use of GPUs to accelerate the computations in Gromacs. We find that this alternative potential has little influence on most of the properties studied, including partitioning free energies, bulk liquid properties and bilayer properties. At the same time, energy conservation is kept within reasonable bounds. We conclude that the newly proposed straight cutoff approach is a viable alternative to the standard shifted potentials used in Martini, offering significant speedup even in the absence of GPUs.
ناشر
Database: Elsevier - ScienceDirect (ساینس دایرکت)
Journal: Computer Physics Communications - Volume 199, February 2016, Pages 1-7
Journal: Computer Physics Communications - Volume 199, February 2016, Pages 1-7
نویسندگان
Djurre H. de Jong, Svetlana Baoukina, Helgi I. Ingólfsson, Siewert J. Marrink,