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From: David A Case <case.biomaps.rutgers.edu>

Date: Fri, 25 Jul 2014 07:17:04 -0400

On Fri, Jul 25, 2014, Sun wrote:

*> In Thermodynamic Integration calculations, several MD simulations with
*

*> different Î» (lambda) values will be performed, for example, for a
*

*> 5-point TI calculation , the values of Î» 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 Î» 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

Date: Fri, 25 Jul 2014 07:17:04 -0400

On Fri, Jul 25, 2014, Sun wrote:

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.

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

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