[AMBER] pmemd.MPI of amber14: run MD twice with the same input but got different output (within statistical error)

From: sun <sun.ntnu.edu.tw>
Date: Mon, 4 Aug 2014 23:39:02 +0800


I know this is not new, was discussed years back, and is NOT considered a problem. But further comments will help us more.

I think in our case, possible causes are:

1). order of addition of forces are different due to network indeterminacy, and the rounding error causes the difference.
2). some verion of FFT which has feature of automatic algorithm selection depending on network condition is used in PME calculation.

For 1), we are running with 24 cores on the CPUs of 12 cores each.

Further comments are appreaciated.

For 2), can someone describe more or point out where ther FFT source code is?

Thank you very much.


AMBER mailing list
Received on Mon Aug 04 2014 - 09:00:02 PDT
Custom Search