This depends on the polymer's glass transition temperature and/or crystallization/melting temperature. If your polymer nanoparticle suspension heats up toward Tg (which is a spectrum of temperatures reported as the mean, not a single temperature), then the polymer will behave in the rubbery or viscous state and the particles will aggregate. Although Tg should be a property of the polymer and independent of the size of the particle, there are several reports showing that effective Tg and mechanical/adhesive properties at the surface of nanoscale films actually differs from that of the bulk (e.g., Tweedie, C.A., Constantinides, G., Lehman, K.E., Brill, D.J., Blackman, G.S., and Van Vliet, K.J., “Enhanced stiffness of amorphous polymer surfaces under confinement of localized contact loads,” Advanced Materials. 19 2540-2545, 2007).
Bottom line: Know the important transition temperatures of your polymer and whether those are reported to vary with film thickness or particle diameter; maintain centrifugation conditions well below those temperatures.
It is very much important. Polymer may undergo change in its physicochemical property and may change into another form. Hence it is recommended to centrifuge at low temperature; usually below its transition temp!
The results will be better with temperature if the polymer is crystalline. If it is glassy, the centrifugation will be effective only above the Tg for thermoplastic. For thermosets, depending on the type of the polymer and additives used conditions have to be fixed.
What is the nature of the polymer or the polymeric nanoparticles?. May I know specific details if you have?