Please keep the email in the loop.
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flexible model is much more expensive than rigid one. If you are not interested in intra-molecular vibration, which is probably the case for shear-viscosity, please use a rigid water model instead.
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If you are using a flexible model, time step at 1 fs is too long to resolve the vibration. It should be at most 0.25 fs.
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1 fs is ok for rigid model.
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The paper I referred studies rigid models, so their recommendation to sampling time/correlation length/simulation time applies to rigid ones only. I can not guarantee the same setting works in your system.
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To give you a head start, try the following settings:
model: SPC/E
variable dt equal 0.001
variable p equal 5000
variable s equal 1
variable d equal $p*$s