AMBER Archive (2009)

Subject: Re: [AMBER] Is the result of sander same as that of pmemd?

From: Robert Duke (rduke_at_email.unc.edu)
Date: Fri Jun 12 2009 - 09:09:45 CDT

Yes, the results are the same within the limit of rounding errors caused by
net communications completion order indeterminancy and specific algorithms
(pmemd uses some splining algorithms that are actually a bit more accurate
than those in sander, so that also causes very slight differences). In
general, you should see the same printout between the two programs for about
300 md steps, roughly speaking, and then rounding error starts causing a
slow divergence into different parts of phase space. You can use the
programs interchangeably, no problems. This has all been discussed many
times by now on the reflector.
Best Regards - Bob Duke
----- Original Message -----
From: "Catein Catherine" <askamber23_at_hotmail.com>
To: <amber_at_ambermd.org>
Sent: Friday, June 12, 2009 10:04 AM
Subject: [AMBER] Is the result of sander same as that of pmemd?

Dear All,

Could you mind to let me know should we expect the results of sander same as
that of pmemd?

Can we do the MD firstly by sander, and followed by pmemd?

Best regards,

Cat

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