AMBER Archive (2006)

Subject: Re: AMBER: Constant pressure - restart - Amber8

From: David A. Case (case_at_scripps.edu)
Date: Fri Feb 24 2006 - 15:18:58 CST

On Fri, Feb 24, 2006, Jennie Thomas wrote:

> Here is the top of my .out file:

If the comments below don't solve the problem, please give *all* of the output
file, up to the first energy. The snippet you gave is missing the information
the system prints about what box sizes it is using.

> a=30., b=30., c=35.

I think that entering this information will override what is in the inpcrd
file, i.e. the program assumes that you *really* want to use these box
parameters. You can readily tell this by looking for the "Box X", "Box Y",
"Box Z" later on in the input file.

Run just a short simulation with ntpr=1, say just 10 steps. That will give
you more detailed information. Try it with and without the line listed above.

[Note that these variables (a,b,c) are not even listed in the Users' Manual,
because under ordinary circumstances they should not be present in the input.
But they are still in the code as a back-door for experts to try weird
calculations. Those that feel a need to can now post comments about how bad
it is to have *any* undocumented options....For Amber 9, I will probably
modify things so that these "experts" have to modify the code to use box sizes
that are different than what is in the inpcrd file.]

...good luck...dac

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