Dear all,
I'm trying to understand how sander splits the workload of a simulation amongst processors, and I'm a bit at a loss. I thought that the idea was to assign approximately the same number of residues to
each processor, but looking at my output, I read
Number of triangulated 3-point waters found: 19880
| Atom division among processors:
| 0 12907 14831 16757 18683 20609 22535 24461
| 26387 28313 30236 32159 34085 36008 37931 39857
| 41780 43703 45629 47552 49475 51401 53324 55247
| 57173 59096 61019 62945 64868 66791 68717 70640
| 72563
For this specific simulation, my protein has 812 residues; the rest is a few counterions and water. From this output, it looks like all the protein residues are given to the first processor, and the
rest is split equally amongst the others.
If I try to run on a different number of processors, I find a similar result: all the protein residues to processor 1, and the rest equally split.
Is that how it's supposed to be?
Thanks,
Charo
--
Dr. Charo I. del Genio
Senior Lecturer in Statistical Physics
Applied Mathematics Research Centre (AMRC)
Design Hub
Coventry University Technology Park
Coventry CV1 5FB
UK
https://charodelgenio.weebly.com
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Received on Mon Apr 15 2019 - 05:00:02 PDT
