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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--
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 - 13:30:03 PDT
