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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat May 18 2013 - 04:30:02 PDT
