Hi Andy,
thanks for the literature links!
Best regards,
Anselm
Am 18.05.2013 22:00, schrieb Andreas Goetz:
> Hi Anselm,
>
> for example these publications by van Gunsteren (there may be others)
>
> DOI: 10.1080/00268977700102571 (section 4.2)
> DOI: 10.1063/1.476021 (section II.D)
>
> In above publications to check for appropriate time steps / integrators or testing the accuracy of an MD implementation.
>
> All the best,
> Andy
>
> On May 18, 2013, at 4:14 AM, Anselm Horn wrote:
>
>> Dear Prof Case,
>>
>> thanks for your suggestions.
>>
>> Do you have a literature reference at hand, where the energy convergence
>> criteria you mentioned have been described and applied?
>>
>> Many thanks in advance.
>>
>> Best regards,
>>
>> Anselm
>>
>>
>> Am 18.05.2013 02:21, schrieb David A Case:
>>> On Fri, May 17, 2013, Anselm Horn wrote:
>>>>
>>>> in their book "A guide to biomolecular simulations" by Becker and
>>>> Karplus, a general convergence criterion for MD simulations is presented
>>>> (p. 79 in 1st edition) without any further reference:
>>>> log_10 (<E(t)-<E>> / <E>) < -3
>>>
>>> I remember this, but never liked the formula very much, since it depends on
>>> the zero of energy, which is an arbitrary value. To me, a more useful measure
>>> of energy convergence (not "general convergence") is the ratio of fluctuations
>>> in the total energy divided by fluctuations in the kinetic energy.
>>>
>>> It is also of considerable importance to examine "drift" in the average value
>>> of the kinetic energy, which can be systematic and considerable, even when
>>> there is an apparent conservation of energy over local time slices.
>>>
>>> Both measure of energy conservation seem to be roughly proportional to the
>>> size of the system, and so are often reported as values per degree of freedom.
>>>
>>> ...dac
>>>
>>>
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>>
>>
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> --
> Dr. Andreas W. Goetz
> Assistant Project Scientist
> San Diego Supercomputer Center
> Tel : +1-858-822-4771
> Email: agoetz.sdsc.edu
> Web : www.awgoetz.de
>
>
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Received on Sat May 18 2013 - 18:30:02 PDT
