Dear Amber Users,
You cannot directly give the velocity in the input file of SMD. But you
have to manage accordingly using the input of what distance you are
stretching the two molecules and for this what is the length of the
simulation.
e.g. if you stretch the molecules 5A (angustrom) (e.g. from 16A to 21A) in
5ns then the velocity is 5A/5ns i.e. 1A/ns.
Similarly, for stretching the molecules 25A in 500 ps simulation then the
velocity is 25A/500ps i.e. equivalent to 50A/ns.
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Received on Fri Jul 24 2020 - 22:00:03 PDT
