Re: [AMBER-Developers] XMIN minimisation and coordinates

From: <istvan.kolossvary.hu>
Date: Wed, 01 Jun 2011 16:04:31 +0200

Thanks, Ben. Good to know that XMIN doesn't do anything crazy.

Best,

    Istvan

Quoting Ben Roberts <ben.roberts.geek.nz>:

> 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
>
> --
> For greater security, I support S/MIME encryption.
>
> Sent from my iPhone
>
> 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 Wed Jun 01 2011 - 07:30:05 PDT
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