Re: [AMBER] Free Energy using linear scaling free energy using soft core,

From: Hannes Loeffler <>
Date: Wed, 24 Aug 2016 12:58:58 +0100

On Wed, 24 Aug 2016 11:01:45 +0300
Markus Kaukonen <> wrote:

> Dear All,
> Nice to be back in Amber (Amber16). Some initial questions:
> 1) Is there any example how to run an absolute free energy
> calculation with pmemd and with explicit solvent using
> Free Energy using linear scaling free
> energy using soft core (numbers refer to amber16 manual) methods.
> So for example: how to calculate the absolute solvation energy of
> ethanol in water using these two methods.

An absolute transformation means that you decouple the molecule from
the environment and vice versa. You simply set scmask2='' (to "nothing")
and run with the softcore feature on (ifsc=1). So exactly as described
by the mdin fragment in the manual. clambda will need to be set to a
useful range which may depend on whether you plan to use the TI
gradient or want to do a FEP style analysis.

Linear transformation for this is generally not a good idea. But if
you want to toy with it: essentially you set up a relative
transformation where all final state are dummy atoms i.e. their vdW and
charge parameters are all set to zero and ifsc=0. It may be most
convenient to set those parameters with ParmEd.


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Received on Wed Aug 24 2016 - 05:00:03 PDT
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