On Fri, Jul 25, 2014, Sun wrote:
> In Thermodynamic Integration calculations, several MD simulations with
> different λ (lambda) values will be performed, for example, for a
> 5-point TI calculation , the values of λ could be 0, 0.1127, 0.5,
> 0.88729 and 1 ( this is the stratege applied in the paper-- "Proton
> Binding to Proteins: pKa Calculations with Explicit and Implicit Solvent
> Models", JACS 2004, 126, pp4167-4180).However,when λ equals to 0 or
> 1, the cooresponding weight used in Gaussian intergration is 0, so
> these two points actually do not contribute to the final result.
I think you are misreading Table 1 of this paper. The CHARMM calculations
used lambda at 0, 0.5 and 1, and did the integration with the trapezoidal
rule. The Amber calculations used 3-point Gaussian integration with lambda
values of 0.112, 0.5 and 0.883. With Gaussian integration, you don't need to
use the endpoints.
> ps: In the Amber online tutorial ( tutotial A6), it is said that the end
> point simulations will be helpful to debug when things go wrong. How to
> understand this ? What useful informations will the end point simulatons
> provide when dubug ?
The endpoint calculations are equivalent to "standard" calculations of a
physical system. If there were some problem with the TI part of the code, it
might be helpful to compare with (say) a completely different code for the
endpoint simulations. In practice, we (now) have extensive experience with TI
calculations, and it is unlikely that this sort of debugging would be needed.
....dac
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Received on Fri Jul 25 2014 - 04:30:02 PDT
