Dear all,
I was calculating translational and rotational diffusion constants of a small sugar molecule. I haven't analyzed them before, so I need some suggestions.
I wonder whether we should image atoms while performing translational and rotational diffusion constants analysis with cpptraj. In Amber16 user manual, it is said that 'In order to correctly calculate diffusion molecules should take continuous paths, so imaging of atoms is automatically performed' in the section of 'diffusion' introduction. But if we wrap the atoms back into box, do we underestimate the movement of the molecule when the simulation time is sufficiently long?
Any help would be highly appreciated!
Regards,Wei
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Received on Thu Dec 29 2016 - 23:30:03 PST
