AMBER Archive (2006)

Subject: Re: AMBER: The PB GB energy from mm_pbsa will be positive on high charged system

From: David A. Case (case_at_scripps.edu)
Date: Fri Aug 18 2006 - 13:35:04 CDT

On Fri, Aug 18, 2006, Suxin Zheng wrote:

> If we want to consider the salt concentration, what's the range of
> the salt concentration in PB and GB calculation should be reasonable
> or acceptable.

This usually depends on what experiments you are trying to interpret.
"Physiological" salt concentration is generally something like 150 mM.

>
> Can we short the "cutoff" in MM calculation and PB or GB calculation,
> such as from 999 to 25. (thus the GB or PB total may be negative)
> Dose it make sense.

This is not a good idea, in my view. Electrostatic cutoffs can introduce
large and arbitrary changes to the energetics.

..dac

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