RE: AMBER: AMBER 6 compilation problems!

From: Ross Walker <>
Date: Fri, 30 Jul 2004 10:30:54 -0700

Dear Grace,

> supercomputer. I noticed that after 900 NSTEPs the results starts to
> differ as follows:

Deviations in MD simulations between different architectures is perfectly
normal. Especially with parallel runs. What happens is you get rounding
differences that propagate over time and give you different (but equally as
valid) trajectories. Typically in order to see if things are running
correctly we only compare the first 10 or 20 steps of a simulation. The SGI
architecture is also very different to a P4's architecture, one is 64 bit
the other 32 bit for example, and so the rounding differences between the
two machines will be more acute than if they were based on more similar

Note, though, if you run the same simulation a 100 times on the SAME machine
you should see identical trajectories. If you don't then something is very

All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |


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Received on Fri Jul 30 2004 - 18:53:00 PDT
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