Re: [AMBER] TI electrostatic free energy]

From: David A Case <>
Date: Tue, 1 Dec 2020 09:08:32 -0500

...quick comment in case it is helpful - it was not clear to me from the
original post what cycle was being used - and if, perhaps, Franz might only
have been talking about one leg of the cycle and not subtracting of the gas
phase, leading to an artificial internal electrostatic energy component that
could be quite large.


On 11/30/2020 1:10 PM, David A Case wrote:
> On Mon, Nov 30, 2020, Franz Waibl wrote:
> > I am trying to compute the free energy of hydration of a set of small
> > molecules at different salt concentrations, using TI.
> >
> > The problem is that I am getting very large free energies (e.g, 130
> > kcal/mol for caffeine, favoring lambda=0).
> Is there any chance that your caffeine molecule has a net charge? It
> would also be helpful to plot <dV/dlambda> vs. lambda: it that
> approximately a straight line? Is that value at lambda = 0.5 about 65?
> I'm really guessing here, but this looks like results for de-charging an
> ion. (Use the "summary" command in parmed to look for the charge
> model.)
> ....dac

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