Re: AMBER: Implicit precision in sander vs architecture

From: David A. Case <>
Date: Fri, 17 Oct 2003 09:05:15 -0700

On Fri, Oct 17, 2003, Teletcha Stphane wrote:

> I have recently seen in my dynamics simulations 'vlimit exceeded' on my
> dual xeon although when using the same restart the calculation runs fine
> on a power4 IBM.
> I know that implicit double precision is used in fortran code, but i
> have no idea of what it means when the calculations are made on 32-bits
> systems (pentium/athlon) or on 64-bits systems (power4, mips, ...).

There should be no differences (in either sander or pmemd) depending upon
whether the *operating system* is 32 or 64-bit. In all cases, all floating
point numbers are double precision.

You need to look someplace else to resolve your problem. A good first thing
to try is to run short simulations on both machines (with the same restart
file), setting ntpr=1, and look to see if you can identify any differences.

Remember that long trajectories will never be the same on two different
machines (due to the nature of Newtonian dynamics), so that it is certainly
possible to have a vlimit problem on one machine but not another, even if
there is nothing wrong on either machine. But repeated vlimit errors are
certainly a cause for concern. Again, this has nothing to do with the sizes
of addresses in the underlying OS.

...good luck...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
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Received on Fri Oct 17 2003 - 17:53:02 PDT
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