Below is a youtube video of 50 nanoseconds long trajectory of a recent all-atom molecular dynamics simulation which I did using NAMD software.
The yellow dots are sodium ions and cyan dots are chloride ones. The silver transparent stuff is water molecules. the simulation was done using the NPT ensemble, which means a constant number of particles, constant temperature, and constant pressure conditions. The SERINE/THREONINE/TYROSINE residues(11 total residues) of Nogo66 protein(structure available here ) was mutated to ALANINE and is simulated here.
!!
Wow!
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