Re: [AMBER] TI electrostatic free energy

From: David A Case <>
Date: Mon, 30 Nov 2020 13:10:18 -0500

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


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Received on Mon Nov 30 2020 - 10:30:02 PST
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