On 12/18/12 1:22 PM, zugunder wrote:
Hi,
I have a general question on cutoff values.
I am using an AMBER03 ff and in a number of papers/tutorials the cutoffs for
vdw/coulomb are reported as low as 0.8 (and up to 1.2 - 1.4 depending on the
interaction type). As far as I understand, increasing this value a bit will
not harm unless there are no errors and may increase the accuracy and
reliability of the calculations. But how do the changes of this parameter
affect computation performance? If I, say, set it 1.0, will I see any
significant difference in speed compared to 0.8?
It is absolutely untrue that increasing the cutoff values will improve accuracy.
On the contrary, you may be breaking the physical model entirely. Use what is
prescribed by the original force field literature or any newer, fully validated
protocol that demonstrates the new cutoff settings and/or algorithms are more
suitable.
In general, larger cutoffs run slower because more neighbor searching is done.
Do not base your choice of cutoffs on desired performance.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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