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Hello,
I am trying to export the marker spatial coordinates after running a simulation. How can this be performed?

It depends on which OpenSim Tool you are using. If you're running Inverse Kinematics, for example, you can set the report_marker_locations property to True. Another method is described in Forum Topic 16938 (viewtopicPhpbb.php?f=91&t=16938).

I want to simulate a reach movement with upper limb. I am using as input the muscle activations (activations over time chart)
I want to have as outputs the wrist and elbow spatial coordinates (where markers are placed) along time, as a response to muscle activation.
I want to generate a file with the spatial coordinates.

You could place markers on the points of interest, then run a forward dynamic simulation where you apply the activations (as excitations), disabling activation dynamics if you wish. You can use the Output Reporter (https://simtk.org/api_docs/opensim/api_ ... orter.html) to report marker locations (https://simtk.org/api_docs/opensim/api_ ... 14e522116b). The User's Guide provides more information about the Forward Dynamics Tool here: https://opensimconfluence.atlassian.net ... d+Dynamics.