The absolute performance of any all‐atom molecular dynamics simulation is typically limited by the length of the individual timesteps taken when integrating the equations of motion. In the GROMACS simulation software, it has for a long time been possible to use so‐called virtual sites to increase the length of the timestep, resulting in a large gain of simulation efficiency. Up until now, support for this approach has in practice been limited to the standard 20 amino acids however, shrinking the applicability domain of virtual sites. MkVsites is a set of python tools which provides a convenient way to obtain all parameters necessary to use virtual sites for virtually any molecules in a simulation. Required as input to MkVsites is the molecular topology of the molecule(s) in question, along with a specification of where to find the parent force field. As such, MkVsites can be a very valuable tool suite for anyone who is routinely using GROMACS for the simulation of molecular systems.

中文翻译：

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MkVsites：用于创建 GROMACS 虚拟位点参数以提高全原子分子动力学模拟性能的工具

任何全原子分子动力学模拟的绝对性能通常受到对运动方程进行积分时所采用的各个时间步长的长度的限制。在 GROMACS 仿真软件中，长期以来一直可以使用所谓的虚拟站点来增加时间步长，从而大大提高了仿真效率。到目前为止，对这种方法的支持实际上仅限于标准的 20 个氨基酸，然而，缩小了虚拟站点的适用范围。MkVsites 是一组 python 工具，它提供了一种方便的方法来获取在模拟中为几乎任何分子使用虚拟站点所需的所有参数。需要作为 MkVsites 输入的是所讨论分子的分子拓扑结构，以及在哪里可以找到父力场的规范。因此，对于经常使用 GROMACS 模拟分子系统的任何人来说，MkVsites 都是非常有价值的工具套件。