AMBER Archive (2006)

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

From: Jennie Thomas (jenniet_at_uci.edu)
Date: Sun Feb 26 2006 - 19:56:59 CST

Thank you, this line was from an input file I inherited. After removing
it, constant pressure restarts are working correctly.

Cheers,
Jennie

David A. Case wrote:

>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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