Re: [AMBER] free energy of solvation of small molecules

From: Fabian gmail <>
Date: Wed, 2 Dec 2015 16:55:43 +0200

Sorry I forgot to ask in each lambda reheating and equilibration, I should use ig = -1, correct?

Or this is neccessary only during production?

best regards,


Dr. Fabian Glaser
Head of the Structural Bioinformatics section

Bioinformatics Knowledge Unit - BKU
The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering
Technion - Israel Institute of Technology, Haifa 32000, ISRAEL

fglaser at technion dot ac dot il
Tel: +972 4 8293701

> On 2 Dec 2015, at 3:42 PM, Jason Swails <> wrote:
> On Wed, Dec 2, 2015 at 7:41 AM, Fabian gmail < <>>
> wrote:
>> Dear Hannes,
>> I bother you again….
>> According to the Kaus paper, it’s clear that only one minimization of the
>> ligand it’s necessary to calculate the solvation free energy, but it’s not
>> clear to me if each lambda value requires a heating and pressure
>> equilibration, and then production, or only one initial heating + equil is
>> necessary and then production continues from the last .rst7 file…. of the
>> last lambda (as in a regular long MD).
> ​In principle, you will always need to do an equilibration. You cannot
> assume that the phase space of different lambda values are the same (in
> fact, they are NOT the same), which means that a snapshot from one lambda
> value will not be an equilibrium structure for another lambda value in
> general. So you will need to perform some amount of MD in order to relax
> the structure to its "new" lambda value and throw out the non-equilibrium
> structures generated on the way to the actual free energy surface.
> The more similar these lambda surfaces are (which you can usually guarantee
> by taking small increments of lambda), the less re-equilibration time will
> be needed. The surface similarity can be a lot worse if all you want to do
> is avoid reminimizing and reheating (which means that even if you have to
> re-do the equilibration when moving to an adjacent lambda value, you can
> usually re-use the minimization/heating results from the previous step).
> That said, heating and minimization are the cheapest parts of the
> simulation (by far). So there's not really much harm in just redoing it if
> you were concerned about it.
> HTH,
> Jason
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Wed Dec 02 2015 - 07:00:06 PST
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