diff --git a/checks/apps/namd/namd_check.py b/checks/apps/namd/namd_check.py
index 2e438ad96..3d981153f 100644
--- a/checks/apps/namd/namd_check.py
+++ b/checks/apps/namd/namd_check.py
@@ -58,6 +58,7 @@ def setup_parallel_run(self):
             # On Eiger a no-smp NAMD version is the default
             if self.current_system.name in ['eiger', 'pilatus']:
                 self.executable_opts = ['+idlepoll', 'stmv.namd']
+                self.num_cpus_per_task = 2
             else:
                 self.executable_opts = ['+idlepoll', '+ppn 71', 'stmv.namd']
                 self.num_cpus_per_task = 72
@@ -122,7 +123,7 @@ def set_reference(self):
                 self.reference = {
                     'daint:mc': {'days_ns': (0.425, None, 0.10, 'days/ns')},
                     'eiger:mc': {'days_ns': (0.057, None, 0.05, 'days/ns')},
-                    'pilatus:mc': {'days_ns': (0.054, None, 0.05, 'days/ns')}
+                    'pilatus:mc': {'days_ns': (0.054, None, 0.10, 'days/ns')}
                 }
 
     @performance_function('days/ns')