Found a solution at http://forum.step.esa.int/t/gpt-performance/460
This is what I did:
snap-conf-optimiser
compute the best system options (the top compute button) and copy the VM parameters from the top line
gedit $SNAP_HOME_DIRECTORY/gpt.vmoptions
paste each parameter from the top line in snap-conf-optimiser to a new line in gpt.vmoptions
Hope that helps others with same issue.
James