Hi,
How inaccurate are the gradients?
How did you test this? (I would test against finite difference gradients
but these are obviously limited in accuracy)
All the best,
Andy
istvan.kolossvary.hu wrote:
> Dave,
>
> I looked at this as much as I could. There is nothing wrong with XMIN
> settings. The problem seems to be that as you indicated sqm gradients
> are not accurate. It bothers lbfgs less, but it kills tncg. The reason
> being that tncg relies on numerous Hess x some_vector products and these
> are computed via finite difference using gradients. Unfortunately, if
> gradients are off (it is probably very difficult to quantify how much
> off is significant) the product won't be just inaccurate, it would just
> not be the product of the Hessian with something. Therefore, the
> conjugate gradient part of tncg runs amok and will never converge. I
> guess, at this point we are stuck with lbfgs for sqm. I tried larger
> lbfgs memory, but it didn't change things too much. What is the reason
> for the inaccurate gradients? Can it be fixed. Even if it is way too
> slow, just to check that minimization works better? I'd be glad to look
> into this some more, but right now I don't have any suggestion.
>
> Istvan
>
> Quoting case <case.biomaps.rutgers.edu>:
>
>> Hi Istvan:
>>
>> About minimization methods in sqm, look at the test case in
>> amber11/test/antechamber/sustiva. (I've attached the sqm input; you
>> can just type 'sqm -i sqm.in -o output-file').
>>
>> With LBFGS, this input runs for 3650 cycles, reaching a final energy
>> of -120.503799 and a gradient of 0.000498. The energy gets to within 0.1
>> kcal/mol of its final value after 2270 cycles.
>>
>> With TCNG, the minimization exits after 10,000 cycles, with a energy of
>> -120.3472 and a gradient of 0.001713. It gets to within 0.1 kcal/mol
>> of its final energy after 860 cycles, but this is still 0.17 kcal/mol
>> higher
>> than the state found by LBFGS.
>>
>> So: this might be the result of gradients that are slightly wrong, or
>> it might
>> indicate that one of the parameters defining the TCNG scheme is not set
>> correctly in sqm. (Or, something else....)
>>
>> ...regards...dave
>>
>>
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>
>
>
>
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Received on Mon Dec 14 2009 - 19:00:04 PST
