I am sorry that my question repeats something that was already wrote in a post above concerning the calculation of water diffusion coefficient based on MSD using coor anal command, but I am having trouble understanding the connection between the:
- number of frames of a trajectory,
- the frequency of saving coordinates in the trajectory,
- the timestep used in the dynamics simulation,
- the skip value used when reading the trajectory in coor anal command and
- ncors value in coor anal.
Are there any guidelines on selecting skip and ncors values depending on the analyzed trajectory features mentioned above (timestep, frequency of saving coordinates, number of frames of the analyzed trajectory)?