Re: AMBER: amber8 parallel sander

From: Robert Duke <>
Date: Wed, 12 Jan 2005 08:03:05 -0500

Yen -
As Carlos says, this is expected. The reason is that when you parallelize the job, the billions of calculations done occur in different orders, and this introduces different rounding errors. With pmemd, you will even see differences with the same number of processors, and this is because there is dynamic load balancing of direct force workload (ie., if one processor is taking more time to do the direct force calcs, it will be assigned fewer atoms to work on). You have to remember that the internal numbers used have way more precision than is justified by our knowledge of parameters, or for that matter how well the method represents reality, and that any one represents one of many possible trajectories.
Regards - Bob Duke
  ----- Original Message -----
  From: yen li
  Sent: Wednesday, January 12, 2005 5:57 AM
  Subject: AMBER: amber8 parallel sander

  Hello amber
  I am testing the parallel version of amber8. I am running an md simulation over a small protein.
  I am testing the calculations on four, eight and sixteen processors. My problem is that, initially the energy values in the output files are the same, but as the simulation proceeds, the values start to diverge making the differences large. Is this kind of behaviour ok or do i need to take care of some parameters.

  Do you Yahoo!?
  Yahoo! Mail - Find what you need with new enhanced search. Learn more.

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Jan 12 2005 - 13:53:00 PST
Custom Search