Re: [AMBER-Developers] XMIN minimisation and coordinates

From: Ben Roberts <ben.roberts.geek.nz>
Date: Tue, 31 May 2011 22:27:33 -0500

Hi Istvan,

Yes. I tested it and found out that it's behaving as expected, though the algorithm seems to do a final coordinate adjustment at the end of each XMIN computation. Thus, the coordinates reported at each step don't correspond to the energies; that's just something we have to be aware of, I think.

Thanks for following up!

Regards,
Ben

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On 31/05/2011, at 12:15 PM, istvan.kolossvary.hu wrote:
> Hi Ben,
> 
> I was just wondering if this issue had been resolved?
> 
> Thanks,
> 
>    Istvan
> 
> 
> Quoting istvan.kolossvary.hu:
> 
>> Hi Ben,
>> 
>>> I believe that's not true. In sander, there's a CASE statement that
>>> sends the code down one path if the value is DONE; another if the
>>> value is CALCENRG, CALCGRAD or CALCBOTH; a third if the value is
>>> CALCENRG_NEWNBL, CALCGRAD_NEWNBL or CALCBOTH_NEWNBL; and a fourth if
>>> the value is CALCENRG_OLDNBL, CALCGRAD_OLDNBL or CALCBOTH_OLDNBL. (A
>>> fifth option, the "default", triggers an ASSERT.)
>> 
>> This might be something new, I must remember an older version, but
>> then this should be fine.
>> 
>>> Have you any thoughts on my other question, specifically: under what
>>> conditions are the lines starting "MIN:" printed out in xminC.c
>>> (assuming the appropriate verbosity is turned on)? I want to be able
>>> to capture the coordinates at those points - where a minimisation
>>> iteration is recorded.
>> 
>> If I understand your question correctly the answer is that "MIN: "
>> lines are printed at each and every minimization step, at the end of
>> line minimization and at that point the gradient is called with NEWNBL.
>> 
>> Thanks,
>> 
>>    Istvan
>> 
>> 
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>> AMBER-Developers.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>> 
> 
> 
> 
> 
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Received on Tue May 31 2011 - 20:30:02 PDT
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