NAMD Wiki: NamdWarnings
So, you've actually looked at your NAMD output and noticed some warning messages. Should you be concerned? What do they mean? A warning usually means that there is something unusual about your system that may require attention.
Warning> Randomization of stack pointer is turned on in kernel, thread migration may not work!
Ignore this warning. NAMD does not use the thread migration feature of Charm++.
Warning: 1 processors are overloaded due to high background load.
This was introduced in version 2.6b2, and occurs during load balancing in situations when there are more processors than patches. The "background load" in this case refers to calculations that the load balancer cannot migrate, not to other processes running on the same machine. The new load balancer recognizes when the speed of the simulation is limited by the unmigratable work and stops shifting the remaining work around in ways that would create additional communication.