What is sufficient time for simulating a large protein system like Kinesin Motors ?
What are the parameters that decide the simulation time is enough. I have heard simulation time is almost 100 ns for bigger protein system
Hi Nashit,
that’s a difficult question. Usually the required length for an MD simulation is coupled to the phenomenon you wish to observe (bond vibration, conformational transition, etc.). Take a look at this figure to have an idea of the time lengths needed for different processes, and the experiments associated to them. There’s also a link between the time scale and the size scale, with different methods being appropriate for each of them, see for example a multiscale simulations of DNA representation here.
The time step is a different thing. It is related to the shortest event in your simulation, usually bond vibrations. Here is where constraint algorithms like SHAKE or LINCS in GROMACS allow you to use a longer timestep. More info about SHAKE and constraint algorithms here.
Hope it helps!
Regards,
-Adam-